It should run ok with '16 cylinder but as the ports etc are very conservative it won't make the same power as a stock de-restricted '28. If the bike is still restricted though I doubt the cylinder will make any difference as they only make 38hp-ish anyway.

If the bike revs freely etc when not being ridden but looses power when being ridden to the point the engine will almost stop then something else is wrong.

Apart from the barrels if the rest of the bike standard? Are the carbs jetted as stock? Has the bike been de-restricted?
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If I have to take the carbs off once more...