Brother, here is what I would try. First, your first posting said, "Ran out of gas, now it runs like ****." Well, eat beans and you will have gas again and if it runs like ****, it probably is. Just lightening up the situation....
Check a few things. Check your ground cable from the battery. Sounds funny to start there, but a bad ground cable weakens the system. Hit a little starter fluid into the intake area (not a lot or it will bind). If starting fluid gets the bike to run for a moment, then you have a fuel delivery problem. Try it a second time. Does it temporarily run? Yes = fuel problem, No = possible spark problem. When you looked at the spark plug firing was the plug grounded to paint or bare metal. Paint is an insulator.
Ohm's Law is simple. Using a 12v system to a 12v system will not cause a problem no matter how large the supply current (I) is available. Your bike will only use as much current as it needs and any excess available supply current will just not be used (V= IR in Ohm's Law). Kurchef's therom helps in the voltage divider therom area. So, if you are getting 11v to places (losing a volt somewhere may be in the grounding area) all your voltages may be short by one volt (maybe not if line loss in one line only is present).
By the way, starting the bike with the plastics off and standing in the rain may be causing a water related short to ground. Get a hair drier and dry off your electrical connections. Don't use a heat gun or you will melt things. Hope this helps.
P.S. Your ignitor will either work or not. There is no in between on CDI units. So, start with the starter fluid and see if she fires. You have a spark (blue is good), so the CDI is working in my opinion. Is my opinion any good? Well, I have been working on motorcycles. cars, machinery and electrical workings since 1974, I have two electronics degrees, I retired at age 46 (closing on 10 years ago) and now I live in the desert of Nevada and drink Jack Daniels on a limited basis - my limit. Take my opinion as you see fit.

 

Jagermeister, I think some gal offered me some once. Seems her and her friends drank that stuff. Not saying its a lady's drink, well maybe I am... Just kiddin'.....
Shadow, I may have 4 college degrees total (besides electronics, I have a BS in Management and one is Liberal Arts), but that does not mean I know jack... Well, maybe I do know Jack on the rocks... I also speak, read and write Korean. Ask a Korean to say the number 18 in Sino-Korean, not Pure Korean (Sino-Korean is Korean made from Chinese characters, yes they have 2 numbering systems and mixing the numbering system with regards to a noun - one shoe for instance - is like being born in the Chola Nam Do area of Korea). Now ask that same Korean to add the word Gnome (or what they call a rascal type person) to the number 18. Goes like this Shim Pal, Shim Pal Nom. Where will you find a Korean to ask? Well, do like I did and spend 3 tours in that country.... How do you learn Korean? Go to the Defense Lanugage Institute in Monterey, CA for a year like the Army made me do...
Red, I went through Fort Devens, Mass. for Electronic Warfare Analyst training. Went from Oct to April many years ago. Still have the picture of Ayer, Mass's homecoming Queen and yes, she was pretty... That area is way too cold for this old dude. Could be that you need to move to the desert of Nevada, from Connecticut, to get that Hurricane working correctly...

 

Shadow, Murphy was an optimist. Sod was right. Murphy figured that everything would turn out wrong. That's being optimistic about the outcome of everything. Whether the outcome is bad or good is not the point. The point is that Murphy knew, through his optimistic view, that it would somehow go wrong - everytime.....
It is so windy out here that when I sent my dog out to go pee, she pinned her ears back and ran back in. I hope that is my glass of Jack with melted ice over there! Dang dog.....
It is time to get on the raft and relax....