Being that you just did a turbo swap and the car is now running poorly it is probably due to something that was disconnected or unhooked during the swap. The car ran fine before the swap (less the turbo grenading) thus it should run fine after the swap. Check the basics first: intercooler/charge piping, pressure test, MAS plug, MAS clamps, spark plugs, fuel filter, etc. If that doesn't do it, drop the downpipe off of the O2 housing and run it for a bit like that. That ought to bring the problem to light.
As far as the metal on metal scraping noise, that's never a noise you want to hear (especially in a turbo car). My guess is the bearings in the turbo are bad and causing the compressor or turbine wheel to scrape on the housing. OUCH!
I've got a 14b off of my Galant and a 14b off of my old Eclipse just chillin' in the shed so if you're interested...
Yeah, lame sales pitch!
If you're not turning up the boost right now on the 14b I'd say to stick with the '61T ECU, MAS and injectors. An EGT or datalogger might not be a bad idea just to make sure you're not overrunning the stock injectors with the 14b. Until you've got a way to compensate for different injectors, MAS, or ECU (SAFC, PMS, SAFR, etc.) employ the KISS method:
Keep
It
Simple
Stupid. Wow, I was all about the acronyms in that post!