J.I.S. bolt heads are often smaller than normal metric ones. For instance, a standard metric M8 fastener normally has a 13mm head. The J.I.S. version only has a 12mm head. You'll find lots of these on your 650. In most cases, the standard one can be swapped in, but it's not going to be 100% correct and original anymore. No big deal really, unless you're doing a 10 point restoration.
One of the most common sizes you'll be replacing is the M6, so you could start there. I'd get stainless and get M6 nuts, washers, and lock washers, along with a couple different bolt lengths. The beauty of stainless is you can cut it without having to worry about it rusting. So, if you get some longer bolts, say 40mm or so, you can cut them down and make any shorter ones you may need. I have cut some down in the past but over the years, I've collected up most of the common lengths needed. But, there are some odd lengths, like the hand lever perch clamping bolts (22mm long). Those you will need to cut from longer ones.
Once you move up to the M8 size, bolts can start getting expensive, lol. I don't have many bolts in that size but do have the nuts and washers.
I also have quite a selection of Allens, both regular and buttonhead. I probably have more sizes of these than regular bolts, lol. They are mostly smaller ones (M4, M5, some M6) because my main use for them is on carbs. Here's a recent thread I did on the carb screw sizes .....
https://www.xs650.com/threads/carb-allen-screws.62686/