Hey Dave,
Don't get too discouraged, most likely your are troubleshooting multiple problems or maybe it is still the Ignition module. It sounds like the light on it wasn't responding properly from what you were expecting. You might call Thunderheart and run it by them. Also, there is a timing adjustment that normally needs to be made as you are setting it up.
The first ignition module I got as a replacement was bad and gave me a different sympton and I ran it by Crane and they swapped it out for me. It would shut down the Front cylinder at different points in the ride. They sent the new one two weeks ago and it has been running fantastic ever since.
With me, I had bad plug wires, the gas tank liner was peeling, the carb had junk it it, then I did an oil change and found the lines were backwards and the oil was being push through the filter in the wrong directions, they also had the oil lines to the tank reversed and the ignition module was heating up and dying. I was ready to sell the dam thing, I was so frustrated every time I saw a Motorcycle on the side of the road I would say, Must be a Big Dog. Now, for the moment and it running Fantastic no issues and I feel like it was worth it, I got the motorcycle where it needs to be mechanically and I got to know my motorcycle pretty well.
Hang in there you'll get there, you are doing great.
Best of luck