INSW20

What year MR2?  Mechanical or electronic speedometer?  On my mechanical speedometer MR2, I'm using an OEM cruise speed sensor for wheel speed input instead of the speed signal from the gauge back to the ECU.

My 3sgte seems very snappy on cold start with E85 retarding the injector timing to spray through an open intake valve, instead of letting the fuel condense on a cold port/valve.  Once hot, my cranking injector timing is same as running, since the ports and valves are hot and vaporize the fuel.

Want to see if this is any better?  Main changes are:  injector timing to spray into open intake valve, a little larger pre-crank prime, and just a large change to crank enrich.  I also retarded cranking ignition timing a little bit.
Volcom86 - e85 cold start - injector timing.pclr

I would say the gain was either very small or zero when that log was captured.  Start with something like this:
  

This seems to work decently well on my 5sgte.  I am running a coil-on-plug setup, which is how I have individual trims and gains on a g4+.

So this car has sat since November 30th, 2019
I just started to try to complete the wiring on the car yesterday.  The long hiatus was due to a fire started by a neighboring suite that burned my business down.  The laptop that had my notes and diagrams and everything was destroyed in the fire.  Finally after 4.5 years I decided I need to finish this car.   Luckily I came here and found my notes, and my spreadsheet.  Otherwise I would have had to start all over.   trying to log what I had planned originally.   
Thank God, I uploaded it here!
I spent all day yesterday wiring what I knew and building a new fuse box that is smaller than the factory Toyota fuse box so it'll fit in the trunk behind the carpet!
Hopefully I can finish the car and have it running before the summer heat hits.

Knock level global is the raw noise level from the knock sensor, this is multiplied by the cyl gain when the specific cyl window is active.  A knock level global of 1000 means the input is saturated, it cant measure a higher voltage.  If your cyl 1 knock level is showing a flat line at 530, this means the knock level global was pegged at 1000 everytime the cyl 1 window was captured.  
Im assuming you are using the stock sensor?, this saturation is common with the Toyota resonant frequency sensors, they usually arent useful with a modified engine.  Swap is for a flat response sensor.  If you already have a flat response, then just turn the main gain down.   

Looking at your map, your pre-crank prime is extraordinarily high for a hot start.  
As a test, can you try dropping the highlighted region down to about 10ms.  See if that help or makes it worse.  If it makes it worse then I would lean towards the issue being related to injector atomisation. 

'IAT Fuel Trim Table': I've got 'Engine Running Time' on one axis and 'IAT' on the other. When hot restarting, the 'Engine Running Time' parameter removes no fuel at 0 seconds, but my full -10% at +40C after 60 seconds has passed. With this approach, hot restarts work well without having to compensate by f. ex. turning up cranking- or post start fuel tables.

Heads up.. you can click on any variable and then press F1.. that will give you a description.
I find Link's help file useful and well constructed.
 
Ign Start Position - The injectors will be opened for the time specified in the Injector Prime Time table the first time the key is turned to the start position.  This ensures that the prime fuel is not injected too early when the key is turned on, then turned to start some time later.  This mode requires a Digital Input to be configured as Start Position and wired to the start terminal on the ignition switch.
 
I'd bump pre-crank prime by 50% and see if it does anything.. If it does.. then lower it until you satisfied with the hot start.
If that doesnt do much.. then go back to original value.. and bump your Crank enrich by 50%.. see how that plays out.. 
Try bumping First crank enrich too.. but just do one change at a time and see which one has the most effect.
You could also change that to Key On and turn the key twice or more in order to gain idea if thats helping. 
 
Also.. I see the car started without much effort on the 2nd crank.. right after it didnt.. I've seen cars with fuel manifolds right on top of intake manifolds or in places where they touch hot parts.. this causes fuel to literally boil and may causes harder starts. 
 
Hope this helps.

I don't know of a basic tutorial, but basically you are trying to change the fuel table to have AFR match AFR target at every cell.  There's a bit that goes into that, but that's the basics.  I start with making it idle and rev, and return to idle ok.  Then I move on to driving low load, and then finally wide open throttle.  Lots of other stuff to set up along that path as well, but that's a basic outline.

Yep, that seems to have fixed it.  Per usual, it's user error on my part.  =)

Yep, that seems to have fixed it.  Per usual, it's user error on my part.  =)

Your log shows gear ratio values of ~125, 70, 45, 33 and I don't think I saw a 5th ratio where your basemap shows ratios of 130, 75.3, 51.1, 36.6 and 29.2.
I would recommend taking a short log of you driving steadily in each gear and repopulating your gear ratio table with the appropriate Gear Ratio Calc runtime values from that log

This guy right here @koracing is the reason the car runs. AMAZING attention to detail! Thank you! 

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.

I would try a name brand adapter like Belkin or Tripp-Lite and see how that does. 
https://www.amazon.com/Belkin-F2CU036btBLK-Certified-Compatible-ChromeBook/dp/B00WJSPWRM/ref=sr_1_1?hvadid=570571498262&hvdev=c&hvlocphy=1027639&hvnetw=g&hvqmt=e&hvrand=8729367719557369245&hvtargid=kwd-349138689568&hydadcr=18032_13462267&keywords=usb-c%2Bto%2Busb%2Badapters&qid=1679611641&refinements=p_89%3ABelkin&rnid=2528832011&s=electronics&sr=1-1&th=1
 
Meanwhile I am looking at laptops that have 9 pin serial ports on them still.... LOL.

Yeah I dont see anything obvious.  I suspect it may just be a lack of fuel due to the overrun fuel cut up to that point.  I would try turning ORFC off and then try to reproduce the problem with that off.  

Your setup sounds very similar to mine, although I'm a billet ct20b on a 2.1L stroker 3SGTE.  That said, I've attached my tune, feel free to compare, but I would advise against copy/pasting the ignition map or anything like that.
ID1050x's
stock gen2 cams
Mac 3 port solenoid
TVIS deleted
billet ct20b, KO downpipe, Apexi N1 exhaust
flex fuel, mainly tuned on E85, haven't done much on the 93 octane map yet
Link canLambda
AEM map sensor
Rife IAT sensor
coil on plug setup using the stock distributor triggers
 

Yeah that looks quite usable.  Trig 2 arming threshold probably wants to be down around 0.2/0.3V to still be reliable when cranking slow on a cold morning or partially flat battery etc.  

Yep, crank sensor is wired back to front.

Perfect, thanks again for the help!

Most likely just a hall affect style square wave. You would probably want the DI pullup off if you tap into the cruise signal.

The speed reading spikes are caused by high frequency noise being picked up by the DI. Try this simple low pass filter circuit below (just if you have some electronic parts lying around). This solved similar problem on mine (though on G4x).

The 3 pin cruise sensor is only used for cruise control but if the cable setup is in a bad way you could theoretically wire it up to the ECU as well and calibrate the ECU to suit. The Power steering does use the speed signal from the dash though so improving that is still a good idea.
On my car I installed a later gauge cluster (needed different plugs) and ran a hall sensor from the gearbox to the ECU with the ECU sending the speed to the gauge cluster speedometer so that I could correct for different wheel sizes. ST18X Celicas have a mechanical to electrical conversion on the gearbox that screws onto the MR2 gearbox too or later gearboxes (with the better synchros and lsd diffs) have hall sensors in them with no provision for a speedo cable.