Adamw

Follow this guide.  https://youtu.be/_P1LRANeO4A
 

Correct.  In G4+ the bulk of your idle throttle opening should be in the main target table, then the idle base position is mostly used to correct throttle position when the engine is cold.  
FYI this is different in G4X just in case your question does not relate to G4+.

Ok, I have made some changes in your map to test some things.  It had a lot of pretty weird settings so we may not be any closer yet.  You are also on very old firmware but we will leave that alone initially.
Can you load this map in, do a store, then turn ign off for ten secs, back on, start the logger, the start engine and see if it can idle on its own.  save that log and attach here.    
evo222 idle test.pclr

That is fine with the single 3 core.  

Yep that will do it.  

25-35% is common, start at 25%.   

Is it on 5.6.8 firmware?  You could try connecting the DI-ve to gnd but it shouldnt be needed.  

Most likely the tune.  Attach the map and a short PC log of a stall and that should give us some clues.

This is normal, they are effectively connected to the same plane in the ecu but it is how they are routed and what current goes though them that is different.  

I believe the Android version of the gaugeart app is already available if you know someone with an android phone or tablet you can borrow.  The new Extra stream has 3 GP temps as requested for your EGT's, as well as all 8 CAN TC's, a couple of GP pressures, 2 math blocks (can basically send anything you like as a math block), 2 digital GP inputs, driven & driving wheel speed, "knock level detected", fuel consumption and all the others that were previously in the .lcs extra streams.  
Set up below.

Leave the -ve unconnected.

I dont.  I would still use those values above though, they will be much closer than using 0.

Yeah you have no trigger signals coming through at all from neither crank or cam sensor.  All your ecu settings look ok so they should be.  It would suggest you have a wiring issue somewhere.  

Deadtimes that we have in our FD below (stock primaries), these would probably be better than having them set to zero.
  

If the coolant temp is below the thermostat set point there should not even be coolant moving through the radiator. 

Thanks for the log, I can reproduce the same problem you have encountered.  It appears to be related to the conversion to AFR.  Since we all use Lambda internally here I suspect we all forgot to test this updated quick trim using AFR units.  You will have to temporarily change to Lambda units (shortcut U).  I will let the software team know there is a problem but the engineer that made this change is on holiday until the middle of next week so we likely wont have a fix for a week or so.  Sorry for the inconvenience.  

Thanks for the log, I can reproduce the same problem you have encountered.  It appears to be related to the conversion to AFR.  Since we all use Lambda internally here I suspect we all forgot to test this updated quick trim using AFR units.  You will have to temporarily change to Lambda units (shortcut U).  I will let the software team know there is a problem but the engineer that made this change is on holiday until the middle of next week so we likely wont have a fix for a week or so.  Sorry for the inconvenience.  

It could be worth trying a "no missing teeth" pattern but my gut feeling is it is unlikely to help.  Regardless of missing teeth or not the ecu still has to predict how fast TDC is approaching based on the time period between the last two teeth events.  When that time period changes by a factor of more than 300% in just a few teeth as it does in those scopes above then there is potential for a lot of error in predicted crank position.   
If I were going to do that I would grind off groups of 2 adjacent teeth, leaving every 3rd tooth to make it the existing 36-2 into 12 evenly spaced teeth.  

I will give an example to hopefully make it a bit clearer.  
These examples are assuming open loop lambda table is enabled and the injector deadtimes are somewhere in the ball park:
Lets say at WOT your afr target table had 11:1 AFR in it, and you had tuned the fuel table so that when operating at WOT your measured AFR was actually close to 11:1.  
Then if you later wanted to try leaning it out a bit to say 11:5afr at WOT, then you only need to change the value in the target table, the fuel table remains unchanged.  The ECU will reduce the injector PW proportionally to the change in target and the measured lambda should follow the new target automatically. 
There are several advantages to using the open loop table - one is described above - you can change the target after tuning without having to retune.  Secondly, having the target factored in to the PW calculation makes your fuel table "flatter", there is less variation from cell to cell as load changes because the fuel table is effectively only compensating for a change in air flow rather than the change in fuel mixture target and airflow combined.  Thirdly, the target can be used as an "extra dimension" in tuning - for example with ITB turbo engines you may have TP as the load axis on the fuel table - but since at 100%TP you could have anything from say 0psi boost to 40psi boost you dont really want to target the same AFR for all boost pressures (you want to target richer as boost increases), so you can put MAP or MGP on the axis of the target table, then even if you are working in the 100% TP row of the fuel table the whole time, you can still vary the target based on boost pressure as well.  

This update is now on the Link website.

This update is now on the Link website.

Use 1JZ vvti trigger mode, offset should be close to zero with that but you need to confirm with a timing light.  
Since you have an idle valve, you will need Equation load source set to MAP and the MAP sensor connected to the same manifold so that the ecu can compensate for the varying air volume passing through the idle valve.  
Turn off CLL until fuel table is tuned.
Turn on Async injection with min async PW = 1.0ms.  And put something like 5 in your accel sens table.  
Assuming it is NA, change your lambda target table so that 0.87 is the smallest value in there (WOT).  I normally have around 095 at idle, 0.9 at 40% TP and 0.87 at WOT. 
For your ign table copy your 60%TP row down to the 100% row, even then it will be on the conservative side.
Also, not related to your running problem, but I would suggest taking a whole lot of rows out of your fuel and ign tables, you are only creating a lot of tuning work by having so many.  For ITB's I usually do TP 0%,2,5,8,11,15,20,30,40,60,100.  Only add extra cells if there is found to be some area that is not taken care of by linear interpolation during tuning.  

Dont overthink it too much.  Set the master fuel to about 6ms, that should be somewhere in the ballpark to get it started.  Once started if it sounds all lumpy then that would suggest too much fuel so reduce the master until it smooths out.  If it only coughs when cranking or fires then dies after a few seconds then you likely have too little fuel so increase the master.  

There is no time scale shown in your picture so Im not sure if filtering would help.  Im pretty sure you could add filtering with a math channel (I havent tested), but that looks like a relatively slow oscillation, so you would need a long filter which would tend to make it feel very unresponsive - especially where you want fast movement such as during a gear shift.  
On race cars where I have this sensitivity problem I usually put Speed Vs AP on the DBW target table, then you have a less aggressive curve at low speeds, and at higher speeds when the ride smooths out you can make the throttle translation more aggressive.  
Example:

sorry i did not explain it right 
the throttle was showing 100% tps with the blade fully closed and 0% with blade fully open 
then i did reversed the polarity and the throttle worked how it supposed to but wont calibrate because it was not closing at all 
the exactly way that you have pointed in the above picture it will go fully open but won't close 
following what you mention about possible mechanism been stick i went to check the throttle body and find plastic shim that goes in between the cover and the gear broke off with that happened the gear was making contact with the cover keeping it at 100% open position
after finding that  broken peace i swap the throttle and it appear to be working fine
will test it again in the next few days and get back to you 
thanks for the tips and sorry for making it so confused