Hyde, it's not just you, you have plenty of company. Stoop, I'm not telling you what to do; as Hyde wrote, it's your motor. But if it were mine, I wouldn't take chances on paying good time and money for a fresh top end only to find that the bottom end and/or tranny was eaten up by grit, or that blocked oil passages would lead to failure. Here's what I'd do.
As anyone who's taken one of these motors down to the cases already knows, once the top end is off it's a quick and easy matter to remove the shift shaft, remove crankcase fasteners, turn the motor upside down on the bench with the top end studs hanging off the edge and supported on block from the floor, and remove the lower case half. After that the transmission shafts and crank assembly simply lift out. If you don't know what to look for in the way of bearing damage, pay a pro to inspect. +1 on flushing of all parts and both case sections, preferably in a proper parts cleaner. High pressure water or steam wouldn't hurt the stripped cases, just be sure to immediately oil the steel bearing journals and blow out all water with solvent followed by compressed air. Otherwise blow aerosol solvent (brake cleaner works fine) through all oil passages and follow up with high pressure compressed air. That's not the best way to go, but 3 or 4 cycles of this treatment will get out most of the debris.
You might think about ordering Hans Pahl's book on the Yamaha XS650 engine from Amazon. It will guide you through breakdown and assembly step by step, and will pay for itself many times over in bullets dodged.
Good luck to you.
.
