Finally, I got the bike running.
I don't know what caused the issue in the first place, but this is what I did to get "fire" to the plugs.
- pulled the fuse for the TSM
- had fire so installed the plugs
- started the engine, the engine only ran for a few seconds
- installed the fuse for the TSM
- started the engine
Everything works fine now, just like it was supposed to. What a pain this has been, but at least I have some hair left for the next time around.
Thanks for everyones suggestions and help, it's nice to know that there are folks around to bounce things off of.