My vote is for the K.I.S.S. theory. It all started with you draining the **** outta your battery, then the bike's charging system couldn't revive it. I don't care what the store told me, I would have replaced the battery..
What are the odds that all these other problems would magically appear at the same time you killed your battery? Know what I'm sayin?
Sounds like youv'e spent a ton of money, and have dropped a lot of time in it.
My vote is to replace your battery with a YUASA, and see what happens.

 

Well gentlemen, the solution was in the carb. Rebuilding the original did not help, and I sure can't figure out what is wrong with it, but a replacement carb has not only solved this problem, but also boosted performance considerably. The stock carb ran ok ( when it ran ) but the new one (slightly bigger) has much better performance too!

After all the hasseling with this problem, it turns out that something went nutty in the carb.

I'm back to the original ign module, and the same battery etc. the only new parts now are the plugs and the carb.

Go Figure.

Thanks for all the advice, and ride safe!

 

Congrats on getting it fixed and back on the road with improved performance.

In one of your posts you mentioned manually raising the carb slide cleared the blubbering.

Sounds like there might be a pin-hole vacuum leak in the carb diaphram.