We've successfully rebuilt many [what we term as] S1 cranks. (87~88 NSR/87~92 RS/NF5) The key point still however, is the centre seal must be in good condition.
A good seal can actually be reused at least twice (we have NF5s that run at the Classic IOM TT that are testament to this), so as long as you don't beat an 87~88 NSR250 to death, and refurb the crank sooner rather than later, they can more often than not be saved.
There are benefits to both types of engine, but if you can, I would strongly suggest retaining the MC18 motor in the MC18 chassis. For the simple reason now, that the more original you can keep the bike, the more it is worth. Even MC18 prices are creeping up now, and a genuine R4J SP is actually a rather rare bike. I've certainly seen far fewer R4's than I have any other SP!
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Andy.
NSR-WORLD.COM
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