JE5 tests the coil pack by hooking up a test lamp between the 12v pwr wire and the grounding wire on the coil. I already had a new coil pack that I installed right after completing all the harness wire tests, so I skipped this step as it wasn't needed. The only conclusions coming from a negative result to JE5 is replacing the coil pack, which I did.
I'm unclear on the effect of "heat-soaking". Are you talking about heat soaking of the coil itself, or another sensor?
As for the transistor location... I'm honestly not sure. Doesn't seem to indicate in any of the information I have either.
I figured the key cycling was the big issue here. Not sure what it means... but it feels important.
Thanks very much for spending some time reading and for the suggestions, it's much appreciated.