650 engine will drop in, but will require the mounting bracket (only one of them, the rest are the same. Forget which. I believe Scott has done this) from the 550. Also, as mentioned the wiring harness, clutch cables, carbs.
The 650 camshaft in a 500 is not worthwhile without the 650 pistons. (Domed in a 650 vs flat in a 500, giving it the desired compression ratio).
Electronic ignition won't give you power. I have it, and its advantage is I never have to mess with points. PAMCO makes a good unit.