Timing is a question that you need to resolve, Sowiuk. For what it's worth I've never seen an XS650 motor spit the carbies out of the boots for any other reason than defective boots from the People's Big Joy Condom Recycling Collective of Tientsin and incorrect ignition timing.
Your first step is to locate TDC accurately. Near TDC the piston "dwells;" that is, it moves very little in relation to crank rotation. Correction for piston dwell is done by indexing. A tentative TDC mark is made, the degree wheel is zeroed on that mark, then degree readings are taken at equal drops before and after TDC. The midpoint of these readings gives you true TDC; for example if the reading BTDC is 4* and the reading ATDC is 8*, the tentative mark needs to be advanced by 2* for the final mark. The drop doesn't have to be large, .040" is plenty. If you use a dial indicator with a long stem directly on the piston it's a simple matter to pull back the plunger while you turn the engine over the top. Once you have the TDC mark scribed, follow directions from the manufacturer of the PMA kit.
Alternatively, reinstall the OE alternator, buy a cam driven ignition, and sell the PMA kit. Good luck to you.