I would get the 550 motor and build it from the best parts out of both. As mentioned earlier - the important bits of these engines are interchangeable. If the 550 turns and has good compression then pick the best carbs/pipes you've got and go forward from there. Keep in mind the carbs are unique to the intake manifolds so they need to stay together as a pair. The 500's, while cool and unique(ish), can suffer issues that really arent worth it (primary chain, clutch & transmission). If you end up having low compression, rings & a hone are an easy enough job - easily done in an afternoon if the engine's out of the bike.
I would also be very weary of a project that someone 'tore down and then half-rebuilt'. Best case you'll have to tear it back down and rebuild it making sure he didnt miss anything, worst case you blow up your engine after investing time & money to get it running. Once you've got a running 550 engine you can tear down the 500 engine and part it out - you could probably get 2-300 out of it that way, while learning about these awesome engines in the process.
Let me know if you end up parting out the 500 - I'll buy your transmission if the miles are low enough. I was stubborn enough not to do the 550 swap when I started my build
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