Hi Brian,
Yep, I've done the full barrel mapping with gearbox karts - that was more to do with designing the exhaust though. As far as the crankcase, I just made sure it was perfectly aligned with transfer ports of the barrel which usually involved trimming the base gasket.
For Rotax, it's the seal that really restricts you having a look inside so obviously you can only put the piston at BDC and work above it, and then put on a timing wheel and work through the inlet port to map against the bottom of the piston skirt. But that's only on the old seal type and to be honest, I only mapped my two 04 barrels out of interest to see how much casting variation there was - both barrels were within a 1/10 on the track.
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