koracing

That's apple discrimination! I am iRate at being iNconvenienced.

Still broken as of right now.
 

Try adding 360 to the offset and see if it works any better.

test
now i can't post anything longer than this
I'll just wait until link's web host fixes this issue

I tried and it's giving me the same error linking it to my drop box.  Site's got issues....

I haven't tried uploading to this site today, but you can always use dropbox, google drive, or similar to upload files and share links to the files on there.

Then what's the purpose of the current interpolate function? In what situation would it be preferable for it to interpolate, but not consider the breakpoints and create a jagged line in a map? If you've tuned 50kpa and 80kpa, and want to interpolate because you think it will be close to linear between those regions, why should the interpolation be non-linear between those points if you have uneven axis breakpoints? Yes this has the same effect as deleting the row/column, but it's just to get it in the ballpark until you tune those sites directly.
I guess I'm the opposite, I don't understand the point of it working the way it does now. It is probably useful for Alpha-N tuning like Electredge mentioned, I haven't got much experience with TPS as load. In saying that, every other ECU software I've looked at uses standard linear interpolation. An option for both would be neat, or an option in the settings to choose "axis scaled interpolation - yes/no". 

That's apple discrimination! I am iRate at being iNconvenienced.

The wideband will pull around 2A so it depends on how good your power to the ecu is.  It would be safer to run it off of a separate relay you trigger with power and ground from the CAN JST4.  The CANTEE should work just fine with the CANJST4.  The problem you will have is the AEM uses 500kb/s communication rate and the CAN Gauge uses 1Mbit/s.  I don't think there's a way to change the CAN Gauge or AEM wideband communication speeds.  All devices on a given bus need to be at the same speed.

That's apple discrimination! I am iRate at being iNconvenienced.

Found it. All 4 wires at the DTM were pinned wrong. Repinned and now works perfectly. Stupid mistake 

A good crank trigger set-up gives 2 main advantages over a distributor or cam-driven trigger.  
Spark scatter - a distributor or cam trigger is generally connected to the crankshaft via several mechancal interfaces with varying levels of backlash and flexibility.  On engines with 4cyl or less especially, valve train resonance can be quite extreme, when you pass through these bands of resonance the camshaft starts bouncing backwards and forwards due to flexibility in the drive system and the cam itself (belt/chain etc) and if there is any backlash in the trigger drive (distributor gears, spline drive or driving dog etc) this resonance is further exaggerated in the trigger signal.  When you have significant scatter it means some spark events will be more retarded than desired and some more advanced than desired so you not only lose power from the retarded sparks, but because you have some sparks that are occurring too early you will reach the knock threshold earlier so you have to run less timing all over as well.  Whereas if the trigger is rigidly attached to the crankshaft there is no valve train resonance influence and no backlash influence, all spark events can be much closer to the ideal angle. Update angle - the angle between teeth affects how far ahead the ecu has to predict crankshaft position, if the crank speed changes between those tooth updates then the prediction is wrong.  The more often you get those updates and the smaller the angle between them, the less prediction error you have.   Depending how bad the trigger design is, both of these can have a big effect.  Spark scatter related especially I have seen some quite unbelievable gains.  The best example I can remember where the only change was the trigger is an RB26 engine I used to work on many years ago, it had an old M8 motec on it.  With the stock 360opto trigger I always knew it had significant spark scatter, but I never considered that an issue and it made around 760HP at the hubs which was more than most in those days.  That was pushing things pretty hard though, I dont think there would have been another 5HP in it if I tried. Anyhow, the spline drive in the end of the cam came loose one day on the dyno which was going to be a big job to fix so we decided to put a crank trigger on it instead.  We made a 60-2 trigger wheel as the Motec was a special "high speed trigger" version (to handle the 360 opto) and 60 teeth was recommended as ideal.  Not really expecting any difference but we noticed as soon as we started it that it just seemed to run smoother, with a timing light on it the spark scatter was now almost indistinguishable.   We played around with it a bit and noticed on the first power run it made more power than it ever had before and the boost had dropped a couple of psi?  I could only link that to the reduction of spark scatter so I tried adding a bit more timing - it seemed happy - so I added a bit more - still seemed happy - then a bit more boost...  From memory it took about an extra 5deg advance over what it would start to knock at before.  It ended up at 880HP at the same boost with the only hardware change being the trigger.   Quite a worthwhile upgrade .
More recently I fitted an atom to a carburetted classic race car as an ignition-only upgrade.  It had OEM computer control ign already but it had a heap of spark scatter and not a great timing curve - I could change the timing by rotating the distributor but it had too much advance down low and not enough up top.  I removed the distributor, added a crank trigger and wasted spark coils. I cant remember the exact numbers but again it was way more than I ever expected, it went from something like 130 to 145HP.  In this case I couldn't say it was only due to the stability improvement though, it got a more optimised advance curve and possibly a better spark or longer spark duration at the same time. 
A good example of the update angle effect is to put a timing light on a Mitsi Evo, these have a crank trigger so no resonance effect but only 2 teeth on the crank.  If you lock the timing and stab the throttle you can see a very large drift in timing during the transient, 5-10deg at a guess.  There is a common 12T trigger wheel upgrade, and if you fit one of these there is still a little visible drift but it is greatly reduced, maybe 2deg.  I find with anything more than about 24T on the crank it is pretty difficult to distinguish any transient drift, some of it is probably timing light delay too.  

<opinion>
I have yet to see definitive proof that in the real world of practical use that using crank position sensors on the crank versus the cam actually causes any issues as when tuning you actually give the engine what it wants and responds to, and whether that value is a degree or 3 off, as long as it's what the engine wants, that seems fine to me.  The only exception to this would be vvti might be a little more sensitive, but most vehicles using a cam mounted crank position sensor aren't likely to be VVT. 
Of course you can go from the other side of the equation and say "what happens when the belt skips a tooth" - with cam mounted sensors you could potentially be throwing timing off by quite a bit, but usually a belt skip won't be in the advance direction I wouldn't think.  Planning around a potential issue like that also seems like the wrong approach.  I would rather address any issues that potentially could lead to a belt skipping versus changing my sensor setup "unnecessarily".
Of course I've always been of the "if it isn't broken, don't fix it, unless it adds a lot of horsepower" mentality.  
</opinion>

I would change your anti-stall gain to a much lower value - currently all 25, maybe try 5, and also raise your overrun fuel cut deactivation rpm table values by like 400rpm warm at least.  Your cold stalling shows the rpm spike from 450rpm to 4000+rpm - not sure if that actually happened or it was a trigger mistake.

Oh, its been increased to 30chars in the next release, forgot I was using that.  

Your currently using open loop for your idle control - what happens if you lower the base position down to zero?  You can try using closed loop as well, but I would experiment with the base position values first to see how the idle reacts - and figure out if you have any vacuum leaks.  Once that is sorted you should turn on idle ignition control which can pull the idle speed down a bit when set properly.

To calibrate the timing you have to click on the little Key that is next to Set Base Timing which will then pop up a "Set Base Timing" window that will fix the timing to the first value in that calibration window as long as that window is open (usually you would use 10 or 15 or something you have a good easily visible timing mark for).  Then you compare your timing light reading and adjust the offset value until both the laptop timing value and the timing light match up (be sure to hit enter when you make a change for it to actually take affect), then once they are synced up you can click ok to get out of that calibration window and it shoudl be good to go.

Check the revision number of your AtomX... if it is Version 3 or newer, it should have the internal knock control module connected to pin 6 - so you can wire the Bosch donut knock sensor directly.

I'm just the wiring guy (at cost for a mate), and had nothing to do with the install, so my job was completed over a week ago. After that I was just a mate trying to help configure the ECU for start-up while it was in my garage, as he wouldn't know where to start, or be able to do it if shown - it's just not his thing. And while I don't have much experience (and none in mapping), I can configure inputs and outputs and follow instructions given on here, so was hoping to get it running on the base map and resolve any possible issues in preparation for professional tuning (which he's agreed it'll need).

When it's idling at the target rpm, the throttle is at 3.9% open but your idle base position is 1.6 with a E-throttle target of 1.5 (total to 3.1%).  Normally I would say you should target a higher value than what it actually requires to idle correctly - like set the minimum E-throttle target to 3.5 and idle base position to 0.8-1.0 so that you get a total of 4.3-4.5 and then the close loop idle will bring it down slightly as will the timing control. Your e-throttle target table looks like it's set up to limit throttle position based on time at WOT, but you can gain RPM targetting to help as well by going to 2 tables and have them switched by your virtual aux 1.  Your base timing table is all 3 degrees around idle.  I don't know if this is normal as I've never fully tuned a rotary engine, but I would increase all the base timing below idle target on the base table to improve it's tendancy to idle up if it drops into the lower rpms before idle control has a chance to improve things.  I'm attaching a link to your tune file modified in these ways you can take a look at or try.
https://www.dropbox.com/s/wkktx1hxwpwk1dc/FD3S_Thunder_MAP_V54-Modified E-Throttle Target.pclr?dl=0

It requires running the car in a non-knocking state that you are certain isn't knocking and adjust the gain such that on WOT to redline you get a range of knock input values starting very low and reaching a maximum of 600-700.  Then set your threshold about 20% or so higher than these values by rpm.

While it sounds simple, making sure you aren't knocking on boost can be a bit troublesome.  Running too little timing can cause more knock noise on the datalog than the corrected timing as well in some cases which also adds to the fun.  On a dyno you can see if the car is making smooth power, an if reducing timing decreases power and by how much to help determine if you are in a "good place" ignition advance wise.  I often wait until I can do several back to back dyno runs to verify if the knock settings and threshold are doing what they should.  The same can theoretically be done on the street but you don't get the feedback of small changes in measured output. 
If the motor is built up to withstand some light knock it is possible to intentionally make it knock on a single cylinder by trimming the timing up on one cylinder at a particular rpm (3D cylinder trim table) and see if you see a corresponding change to measured knock levels in the datalog.

There needs to be cause and effect.  If you're the wiring/install guy and he's saying he wants you to get it up and running then you're in charge of what that requires.  If it requires changes be made or it won't work right, and the customer doesn't want to do those things to make it work right, that's a stop all work and not have your name attached to it type of thing in my book.   Yes someone with some experience tuning needs to get involved - it can be locally or remote - but the customer will likely need to be prepared to pay for this to happen.  The owner can sign up for HP Academy or similar online training if he is so inclined, but none of the options to get the car dialed in are going to be free. 

There needs to be cause and effect.  If you're the wiring/install guy and he's saying he wants you to get it up and running then you're in charge of what that requires.  If it requires changes be made or it won't work right, and the customer doesn't want to do those things to make it work right, that's a stop all work and not have your name attached to it type of thing in my book.   Yes someone with some experience tuning needs to get involved - it can be locally or remote - but the customer will likely need to be prepared to pay for this to happen.  The owner can sign up for HP Academy or similar online training if he is so inclined, but none of the options to get the car dialed in are going to be free. 

I would love to help you get this sorted out, but you're not really responding or acting on the information that has already been provided.  I do not undertand why you appear to not want to post your tune file.  That's not really a big deal if it's just a 3ms master fuel change on the RX7 S7 base tune provided by Link. 
All that being said: you or anyone you get to help you aren't going to be doing any tuning without the wideband connected to the ecu.  You have a coolant temp sensor issue which does affect enrichment and thus can throw off fueling so making any changes while that is reading incorrectly is an issue that can cause you to end up chasing your tail while tuning. 

Please do the following: Test the coolant temp sensor and wiring - repair the wiring or the sensor.  Connect the wideband analog output to your ecu.  Take a datalog with those things functioning in the log.  Once those are working correctly post the tune and a datalog of startup/idle here.

You would set it to the 1000kpa/150psi TI sensor calibration.  You can change units in the user preferences to PSI to get 43.5 or you can set it to 300kpa which is the same setting in kpa.

Took quite a bit of time to go over everything and make sure it was set up for success down the road.  Not everything was just to make it run.