The drive shaft between the engine and transaxle could be broken. There have been reports of this happening a couple of times in this forum.
I'll check with Techstream tomorrow but the 12v is new and on a trickle charger and the HV battery is fully charged too.
Interesting. I don't see how that could be the problem though. The car was in use daily and I thought I'd install new sparkplugs and injectors and it hasn't really run since. Over my troubleshooting attempts to get it to run though, the HV battery went badly depleted which led me to pulling it, removing bus bars, charging all modules and replacing a few after multiple discharge/recharge efforts. Thanks for the info though, I'll research the driveshaft thing.
There is a spring loaded damper that slips and makes the awful rattling while misfiring. It could be broken and has happened before as Brian noted. If the above was allowed to happen many times as the hv battery drained, the damper springs could have failed. Rare but possible. Even more unusual would be something jamming the engine as a result. I suspect a very basic fault happened when you took a good running engine and changed coils and injectors. Maybe a pulled wire on the coil wiring harness or a cracked insulator on the plugs. Backtracking then would have been a good move. That problem is probably still there. I must say that was a good move although who knows what the parts car had for a hv battery. Codes could tell the story.