So, I've got an update.
I rechecked all my wiring, all looked good, proper connections tested for continuity with a multimeter, everything was perfect. Still made no difference. Unplugged the coil and the electronic ignition system and ran to a separate battery. No difference. Found out that I didn't build the wires correctly.
Redid coil and boot ends this way:
http://www.xs650.com/forum/showpost.php?p=180156&postcount=2
Still no difference. Ok, back to basics. Spark, Air and Fuel.
Spark? Have spark. Looks strong, tests with simu plug tester widget grounded properly. Plugs are brand new. Check.
Air? I'm breathing and it's got less than 500 miles on air filters, Check.
Fuel? Lines are set, hoses in place, filled with fuel, and let's not forget -- I drove this bike home with it's bad charging issue after being at a random strangers house for 45 mins while we let it charge...
Well, since I'd beaten the spark issue to death, and it's going to have air. Pulled plugs, both dry......... let's try some starting fluid. Vrooom, started right up. So, obviously something wrong with the carbs now, plugs were dry.
Can't make this kind of sh*t up can you?!!!
Pulled the carbs, I've started taking them apart. In the bowl of one of the carbs I've found what I can only guess is remnants of my old air filters that were in there when I first started tinkering around again on this bike. Yum. Guess I'll learn to actually rebuild the carbs now!
Dave