I'm in your same boat on my '78 750K.  After getting it back together in April, it was leaking a bunch, so I decided to completely tear it down last week.  Everything is off to powdercoat, and I plan on diving into the motor tomorrow.
Only you can answer the stock, cafe, brat, digger, chopper question.  I've learned it depends largely on your mechanical (and tool) availability.  I tore down a CB550 nearly two years ago to cafe and it has become a garage lizard due to a need (and my inability) to weld, fabricate, fiberglass, etc.  
Keeping the 750 stock has been a much easier endeavor.  What comes off goes back on, and it fits!  Downside is finding some of the stock parts.  Your call.  Just have fun doing it!