Well, I had a chance to do what you are having problems with and mine has no problem, so it's not just a hidden Mustang "characteristic".
It may just be a characteristic of your cam and head combo. I think you should check your TPS, though, just to be sure. To be honest, though, I would probably just not worry about it. As long as the engine runs well otherwise.
As far as the air pump goes, I think it would be less costly to just get an off-road h-pipe or x-pipe. You've already pretty much removed all of the emissions stuff anyway. Otherwise, the only thing I can say with certainty is that all the thermactor plumbing would have to go back. As to how to do that with your heads, I can't say since I don't know.
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351W 89 Mustang GT Convertible