So putting the cam in upside down would not change anything?
That's right. For every full 360° rotation of the crank, the cam rotates 180°, a half a turn.
Consumer-oriented service manuals generally are not written very well for the newbie mechanic to learn from. As such, the astute members here have acquired all the available manuals to try to cover all the bases when it comes to meticulous procedures. I generally consider these manuals as reference points, reminders if you will, because they're not written very well.
I had one manual that, I swear, was nearly useless. Half of the print was a large cautionary paragraph about 'disconnecting the battery ground', repeatedly inserted before every section, even if you were going to just empty the ashtray. And when it came to doing a complex procedure, it gave no detail, like 'remove engine from car', with no info on how to do that.
Maybe you could use more manuals. Find some here:
http://www.xs650.com/forum/showthread.php?t=41
There's also an online course that will give you a better conceptual understanding of these things:
http://www.xs650.com/forum/showthread.php?t=31638
Back to your problem. One thing you could try, after you get it back together, is to turn off the fuel delivery to the carbs after it starts, so it's running on just the fuel in the bowls. As fuel is used, the fuel level will slowly drop. If the engine runs continuously better, then you may have identified an overfill condition, caused by bad floats, float valves, height setting, crack/leak in carb body, warpage of carb body, ...etc.