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Have you checked for intake leaks. Might want to spray a bit of carb cleaner around here and there when it is running. I had an 89 that ran poorly and we traced it to an intake leak. Took off the top and sealed it and put it back on and it ran just great.
Going from a 350 to a 383, especially if it's a MAP system, should require a ECM re-program.
However, if the engine ran well at first and now doesn't, something has changed. Finding it is the task. That's the part I don't understand; how it could have run well and now doesn't.
Most agree that off-the-shelf aftermarket PROMs don't work well I'd give Alvin at PCMFORLESS a call. Be prepared to have ALL the engine specs at hand and he can straighten out your ECM programming.
Also, with the changes you've made in the engine, I believe that the "0" degree of base timing is now out the window.
Is anyone running a 383 with "0" degree base timing? Please chime in.