Sorry for monopolizing the forum. My head is spinning. Each answer opens up more questions.

So rather than rebuild my MC18, including scavenging parts, I am looking at a complete running MC28 engine. Will it run OK with the MC18 carbs, PGM I, etc.? Does this make sense for a track/race bike?

Specsheet says the 28 has a slightly higher compression but less power. I am guessing this could be because the top of the exhaust valve is a bit lower? If so is this in the barrel itself or a thinner base gasket? Are the barrels and heads interchangeable?

Is there some resource that lists all the combustion chamber, porting, crank case, timing and other detailed specs for the various models?

From memory yes the MC28 motor will go straight in but you will have to identify the neutral wire from the GPS (gear position sensor) for the MC18 wiring loom and you will need the flywheel and pickups from the MC18 which should fit without any issue. I wouldn't be too worried about compression or power....should be very close to an MC18. From what I have read most of the problems with liberating the power from an MC28 come from the electronics and pipes.....

88~97 (MC18~MC28) motors share similar crankcases, with the same frame pick-up points, meaning that any motor will fit any frame. (The MC16 motor has the same pick-up points, but has solid mounts and isn't a direct fit in any other chassis.)

The best porting of all models is the 1989 R5/6K.

As geezagillard says, it's really not worth you damaging braincells worrying about porting/compression/ignition timing etc., as it's going to make no noticeable difference to an otherwise standard bike. What you do want to worry about with any kind of mix'n'match however, is that the RC Valves operate correctly. Make sure that once it's all up and running that you [a] have the required slack in the cables, and [b] have full sweep of the valves. Not all RC Valves are created equal! This may mean you need different cables or servo, or both, depending on your final choice of components!

At the end of the day, you're just going to have to make a decision, jump in, and figure it all out! Most people just rebuild or source the "correct" replacement engine, so you are asking questions most people don't know the full answer to!
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Andy.
NSR-WORLD.COM

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Thanks Andy, much appreciated.