Help me diagnose last couple bugs on the swap.

I think first thing I'd do is rig a pressure gauge and monitor fuel pressure. Second is change the coil. Some of the guys on here know I dislike "throwing parts" (and money) at a problem, but you said the resistance is out of spec. That, and the symptoms, would be enough to convince me.

"Wrenches" in the gears.........

What year/ make model is the car body?

What are you doing for fuel tank venting?

Other things I'd do, even if you have to "rig" something, is monitor voltage to the ECU and whatever supplies the coil on startup, and get a spark tester and confirm that you are actually getting a good hot spark during start.

If you cannot do anything else, make certain the coil is getting full voltage in crank.

Make sure the ECU grounding is properly done. (And for that matter all of it.) Is the battery grounded direct to the block, or rear mount, or what?