PCM wiring

Well first, part (or even all) of your problem might be right in the car---nothing at all to do with the "new" harness

Here is how Mopar ignition switches work.

You have main battery in, and outputs are:

"ignition run" (ign1) which powers the underhood "stuff" like ignition, alternator field, and VR but is hot ONLY IN RUN. This wire goes DEAD during 'start'

"bypass" or (ign2). This is the normall brown wire that goes from ign2 at the igntion switch to the coil+ side of the ballast in stock harnesses. This is hot in 'start' and bypasses the coil relay AND IS THE ONLY SOURCE of ignition power during 'start.'

"accessory"---hot in both "run" and "acc" positions of the ignition switch, also goes cold during 'start'

"start"....normally yellow, feeds out into the bay and keys on the start relay

NOTE: The 'start' yellow wire and the bypass 'ign2' are both hot at the same time but ARE DIFFERENT CONTACTS in the switch to avoid backfeed issues