The test wouldn't fail, but it's unlikely you overheated something.
The wiring on your JDM is identical to the wiring diagram on my site. You have NO sequential fuel so don't use the sequential wiring diagram though.
If you don't want to cut up the wiring on your AFM connector, I suggest you use fuel pump method 1. It's a bit harder because you need to stick your head under the dash, but at least the wiring under the hood stays intact.
Same thing for the air temp sensor. Instead of bringing the air temp signal in through the black and red/green wires of the AFM connector, it's much simpeler to use the wire for the power steering pump instead. That wire is not used, regardless if you have power steering or not.
Find the blue/yellow wire in the front of your engine. If you have PS, it goes to the PS pump. If you don't have PS, it's tied in a loop near the thermostat house.
Connect that wire to one of the two air temp sensor wires (it doesn't matter which) and ground the other air temp sensor wire to the throttle body.
Your air temp signal now comes in on pin 1P (blue/yellow) instead of pin 2P (red/green) so change your wiring inside the MS3 accordingly. IOW, inside the MS3 case, you need to connect mainbord pin 20 to 1P instead of to 2P.
Looks like you've got everything covered except for the DB9 and the LEDs.
If you want to use these, you need to install everything with * and ** in my instructions here: http://westfieldmx5.devocht.com/mega...ms3/99-05-ms3/
Basically, install all components on the left side of the 40 pin connector in your first picture.
It seems I forgot to add that option in the 90-97 instructions.