I believe that if you take it to a powdercoat shop that does regularly motorcycles, they should be able to strip the paint and do everything right. Motorcycle frames are not that different from bike frames except that they are bigger and they have even more doo-dads and threaded holes. The motorbike customers are probably just as demanding too.

I had an old bianchi powdercoated and was nervous about it until I walked in the shop and saw a number of gleaming motorbike frames all perfectly powdercoated that had been carefully masked in all the right places.