That black cloud usually indicate a rich mixture, considering the problems you are having with the computer, I'm not surprised. I wouldn't worry about the smoke, it will likely go away when you get the other problem fixed.
It does sound like a computer problem, that would also cause the EFI to look bad. May I suggest, before ripping out the EFI, go to your local salvage yard and get another computer. It's not as expensive as new, so if it doesn't fix the problem you won't be out too much (Won't be more than $150), but I believe it will cure your problems. A buddy of mine has a 89 Cheroke (sp?) that was doing the same thing, bogus codes, running like crap, 45 mph tops. Got a used computer, running like a top for more than 2 1/2 years.