Sounds like the throttle body is mis-adjusted. The adjustment screw on the butterfly flap (throttle stop) can become mis-adjusted. This means that the throttle will stay closed and when cold, will start OK, and when warm, will be hard to start.
Is the tuner file written to correct for the 42" injectors?????
If not, this can cause problems. Usually not the problems you have.
Try setting the screw for the throttle plate correctly.
Here is the procedure:
Start the car.
Disconnect the IAC connector from the IAC motor.
Turn the screw down that is by the IAC until it bottoms out.
Then unclip the throttle cable from the throttle body.
Then adjust the screw (it's an allen key) that stops the throttle stop.
Adjust it on the idle is about 700rpm for manual or auto.
Once this is done, reconnect the IAC connector and throttle cable.
Test the car and see how it is.
Good Luck.
Don