For the trans, all the pcm does is trip a couple solenoids when conditions are right, and it pays attention to speed/engine rpm to decide if they are working or not. If the solenoids delay engagement, or don't engage at all, the PCM will set the codes. The delay is measured in small parts of a second... so, something as simply as a dirty valve body may be responsible.

Look at the wiring diagrams in the service manual. Put the wiring back to stock. Start from there.

 

That large red probably really goes to the starter.