UPDATE
After letting it soak overnight, I reassembled the carbs. Made sure I rinsed every piece, as well as blew compressed air through everything. I took my time with this as I didn't want to miss anything.
I followed the steps in post #4 in this thread, before I put them on the bike.
http://www.xs650.com/forum/showthread.php?t=17794
I also put on pipe tighteners on my carb boots as the tighteners that we're on there we're old and breaking. I also took the spark plugs out and brushed them off to make sure I had a good chance of starting.
It fired right up, I still had the spitting/puffing issue. But I think because I had betters carb boot clamps, the carbs didn't pop out. At one point the revs shot up to 3-4000, And I unscrewed the idle screw to lower it. Thats when I noticed the spitting/puffing either stopped or diminished.....Eventually after a few minutes of warming the bike up, there was no more spitting/puffing.
I decided to try and give the dead cylinder method a go. Like before I couldn't get the left cylinder to fire, but had no trouble with the right. I switched plugs to see, and the right was still fine. I then switched the spark plug in the left cylinder with 2 other ones I had (they we're used though, and we're kept for testing purposes). So I had tried 3 diffrent spark plugs in the left with no luck. I then took the right spark plug and put it in the left, and it fired right up.
So obviously I need a new pair of spark plugs. I currently have NGK BP7ES.
But other than that, so far...the bike is running again. Even though I know i have some issues with the bike to work out, I can't help but smile from ear to ear to hear it fire back up.