Ttpcar

Something like below will be a starting point.  Set the "upshift digital input" to the same input as your clutch switch.  Make sure you select "NO" when it asks you if you want to disconnect the clutch.  This will just give you a cut for the whole time the clutch is down.   

Will need to see a log and the tune.
Did you set Lambda 1 to "Link CAN"?

As I mentioned above, pin 5 is connected to the calibration resistor that is in the back of the connector, it doesnt have a wire to the sensor.

You really will need to do some tracing of the loom to see what is connected, there is very little documentation for the HKS looms especially in engish.  But in my experience for most of the cars with CAN bus, auto trans, or Dash communications they are set up as a piggyback only just controlling fuel and ignition, so you will likely find idle valve and fan is not connected to the Link.  Temp gauge will also likely be via Toyota BEAN communication from the factory ecu.  
I would expect VVT should work though.  Set up looks correct.  (note it wont work at idle because the lockout is set to 1300RPM so you could try above that.  Test wiring with the engine off by switching the Aux 2 to "Test PWM" and frequency to 10Hz and see if you hear the solenoid clicking.  If it clicks then it is just a matter of tuning it.
Also, not supper important, but set the firing order to 123456, the HKS looms have the injectors wired in an the firing order rather than 1 to 1, 2 to 2, etc.

Apart from a Aux connected to a DI, CAN would be the only other option.  You would loop CAN1 to CAN2, send a Virtual aux that is true when TC knob pos = 0 out of one bus and receive it into the other as "Traction disable".

You can connect to any unused analog input.  You could use one of the original front O2 sensor signal inputs, the MAF signal input, or there is one on the expansion connector.

If you want to add an extra fan step for fan 3, you could set the base position table to 3D, put virtual aux 1 on the Y axis.  Set up the virtual aux to turn on when the ign 4 fan is enabled.  Example below would remove 30steps from the base position when the fan switches on.

I would not attempt to use antilag unless you have at least a single EGT.  You will also need E-throttle or a throttle kicker and you will need a pedal box with non-vacuum assisted brakes, or an electric vacuum pump for the booster.  

Ah, it looks like you may have trigger 2 set to hall effect.  Can you change it to reluctor and try again.

Here's a quick video to give you an example.
Gear shift knock.mp4

Also have a look at the new CAN one from 14point7.  I have been testing a pre-production one for him for 6 months or so and it is great.  About the same cost as AEM but uses the newer LSU-ADV sensor.  Uses the same CAN ID and structure as the Link CAN Lambda so is easy to set up.  https://www.14point7.com/products/spartan-3-adv

You can set the trim tables up however you like, but an example below would allow CLL to add 15% fuel when above 90%TP or remove 5% fuel when above 90% TP.

I dont think the log shows it stalling so we may not be seeing the real cause, but a couple of things I notice: 
ISC RPM lockout is set quite high @1500RPM, something like 400RPM would be more normal.  This lockout is added on to your target idle RPM, so if your target idle is 1000RPM and your lockout is 1500RPM, then the ecu will try to take over idle control at 2500RPM, closing the idle valve trying to bring the RPM down to target.  Also, the minimum clamp needs to be set to 15% on these valves. Your Aux 2 frequency is set to 100Hz (I notice our E36 base map is also), that seems lower than expected to me.  The last car I tuned with the bosch 3 wire valve I used 200Hz and had good control range.  There are some odd spikes of low ignition dwell recorded in the log.  This may indicate a trigger issue.  Can you do a triggerscope at idle.  

Yes it is now ok to run the current release.

@Adamw I try to get some data for you! Perhaps the video already tells you enough. I talked to my VW/Audi guys...it is no problem to use these actuators on RS3 with upgraded turbo to ~2,5bar boost.(Tested!)
 
 

Yes, I have a pretty complete E46 M3 CAN setup.  I will post it later when im at my pc.

I'm overseas on holiday so have only had a brief look, but the first thing I see is the MAP is reading wrong.  As per the manual you need to make sure all inputs are set up, calibrated and reading correctly before starting .  It should read near 100kpa with the engine off, yours is reading 25kpa.

The Dodge Ram settings from the help file are usually quite a good starting point for most of the Bosch throttles.

Can you point out where?  I had a quick look and it seems to match to me...

I assure you all we will let you know once we have it out.
Would rather have it all well sorted so we don't make the same mistake again.

i am looking for a ecu to run my 1998 lexus gs300 with automatic transmission and has the 2jzge vvt-i fitted.
 i have turbo'ed this engine using a gt35 turbo and i am going to be forging it and running stage 3 brian crower cams  so i need an ecu that will run a 2jz with vvt-i and a auto gearbox if anyone can give any guidance, thank you.

The engine fan system does vary across the Evo 4 to 9 models.
Most Evo 4 to 6's will have the engine fan work by grounding pins 20, 32, and 34 through Aux-Ignition 4.
Some Evo 7 and 8's and all Evo 9's will control the engine fan by applying a PWM signal to pin 21 via Aux output 1. I believe 100% in the duty cycle table will give 0% fan and 0% in the table will give 100% fan. The relationship is inverse.
Scott

Finally after far to long we have some recordings off the G4+ KnockBlock
These recordings are off our well abused 1UZFE VVT test engine.
 
 
Engine background noise.m4a
Mild Knock with bad tune.m4a
Severe Knock with bad tune.m4a

unable to configure my aem uego wideband with my link g4+ as i have mentioned this problem in my previous post .
this is how it is at the moment 
wideband configure as analog volt 5 as wideband 
function lambda 1
calibration cal table 4
low volt is 0.00
high volt is 5.0
error value value 34.464 lambda
Cal table is 
input value A 0.00v
input value B 4.25V
output units Lambda
output value A 0.683
output Value B 1.264
what am i doing wrong its not showing as my aem wideband showing afrs

We could likely guide you to what is needed to be done.
Flick an email in and we can do you a picture of what's needed.
Its a simple as soldering to the pins that are used for knock a couple of wires.