Maybe try unplugging the thundermax and plugging the stock ecm and see if she fires. I'm sure someone with more knowledge than me will chime in. Hopefully you get it sorted out.
I have the four wire plug, which one should I check?Check the center terminal of the 3 wire plug at the coil for 12v +, with the key on and kill switch in the run position.. this will determine if power is present at the coil..
Look what I found.
99949-08_en - 2008 Wiring Diagrams | Harley-Davidson SIP
Y/GN is the power wire. The 4th wire is Ion Sense.
Shiite, If it's that easy, I might even go looking for my own.