To be perfectly honest, while you could, possibly get it to eventually run, I wouldn't waste my time with the MC28 carbs and air correction. They're great on a stock MC28, but a terrible idea for anything else. You idea to revert it to MC21 is bar far the superior option, in both simplicity and performance.
The MC21 and MC28 TPS is essentially the same, but the initial position may be set differently, and it's all about resistance/voltage from it to the PGM. You can try going through the 87-93 Service Manual to try and get the output the same, but all the air correction and jetting is very "wrong" for the MC21. You also need to consider the expansion chambers. If you are using stock MC28 chambers (to clear the Pro-Arm), they (and the silencers) are heavily restricted, and will also affect setup.
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Andy.
NSR-WORLD.COM
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