It sounds like the engine is blowing black smoke both in neutral and under load, is that correct? You need to have an oil analysis done so you can confirm whether you are getting diesel in the lube oil, could point you in the direction of the problem. A turbo shop should be able to bench test the turbo to determine if it's performing properly off the engine (developing proper boost). Klem might have something there about a leak on the intake side, especially since all that stuff was r/r'd for paint.
SV Laurie Anne
1988 Brewer 40 Pilothouse