Acura V6 misfire case study: (SI Ep 8.1)

We're back on Staten Island, visiting Keith DeFazio, for more weird and wonderful adventures in automotive diagnostics!
This old Acura is running rough after a recent engine swap, and setting misfire codes. A lot of variables here, but let's try to sort out the cause and effect.
I admit that in this case study I ended up taking the "scenic detour" to get to the root cause of the problem. However, I think that for educational purposes, nothing beats a "scenic detour" :)
Enjoy!
Ivan