Here's my plan. Keep the black box ecu installed and do some learning with it.
The 0411 i have was tuned by black bear using EFILive so i'll need to find a HP Tuners starter tune for the 0411. I think.
You can find a 0411 tune pretty easily in the HP tuners repository I'm sure.
Some things that should be looked at between your BB tune and a factory tune:
Max RPM possible for every gear to ensure you cannot overrev,
Injector firing timing position
Actual engine displacement per cylinder (good if you're bored over or something)
Things like your VE table will not be able to be directly compared with the black box map. I think someone around here made a converter, I was also working on one but it's not finished, so it may be possible to compare this way.
A handy tool in the tuning suite is in the scanner there is a way to manually control the engine and transmission... so while it's idling, or even being driven, you can force a commanded engine speed, spark advance, kill injectors one by one, lock the torque converter, etc.
I'd start by figuring out the idle speed and spark advance your engine likes at idle at least. The injector toggle function may be helpful in seeing if the effect of dropping #4 or #7 cylinder is the same as dropping another... so this can help you realize if issues are fuel or spark related too.... or if the ECU even notices misfires for the correct cylinder.