Man I would not go back to stock.
I have BS38s (76-77), ran them on my tired motor and they got the job done. Then I tore it down, rebuilt with 707ccs, added shell cam, and now the thing simply won't idle unless I run a stupid huge PJ (137.5). I can get it to crank first kick, feels fine at WOT and midrange, but the motor will pop stall randomly at idle throughout my ride if I don't run an obese pilot jet. That's when I bit the bullet and picked up VM34s.
I would work with the VMs. They are simple, and from your post it doesn't appear that you've taken the time to learn how they work (no offense). Pull off the float bowls, unscrew the lids, and check your jetting. XS650 specs are as follows:
Needle jet: 159 series, P5 or P6
Pilot Jet: VM22/210 series, sizes 20-25
Main Jet: 4/042 series, sizes 180-200
Stock vm slide is a 2.5, works well for XS.
If you haven't inventoried your jets, here is how they come from Mikuni bone stock:
Main jet: 4/042 series, size 260
Pilot jet: VM22/210, size 35
Needle: 159 Q-2
Needle jet: 6dH4
My point is that these carbs are a custom application and the old racers have already figured out the best jetting formula, and it's completely ass backwards from how the VM34 comes from Mikuni out the box, so if you're not sure what's in there it's all just a game of cat and mouse.
Another point to consider is that every single "XS650 jetted" carb kit out there save for 650central and CycleX is jetted too lean. To make these run right on the XS you've got to have them jetted per the specs I posted above.
Fouling plugs you say, tells me maybe you're still running the stock 35 pilot. Or perhaps your floats are outside of the specified 22-24mm height.
Also, read this shit front to back: