[TurboKraft]

Scrap the CIS, install the EFI. Zero issues starting up and breaking in a new motor with a new EFI.
As you said, if you go with AEM from TurboKraft, we'll give you a start up calibration file. Actually, the tuning file will probably be based on another similar build we did here, so 90-95% perfect, only light touch-up needed.
If you go MS, there are people on this forum to assist.

Either way, you'll be dumbfounded at the difference it makes.

Also, the Carrera manifold doesn't always make the colossal difference people expect. There's a lot of other parts and prep needed to make that a worthwhile upgrade over the flat manifold and EFI Injector Blocks. If you want to review the +/- on this, give me a call.