First, try backing out the idle mixture screws a bit at a time. I find it works best for me anyway, to adjust one side for best idle speed, then readjust the speed and go do the same for the other side. Readjust the speed again, then go back and repeat the process to get a bit finer adjustment.
Speaking of thunderbike, the one thing that will do the most to wake up the Scrambler engine is a set of cams. It looks like they use the same valve timing as the 900 Speedmaster engine, and that will diminish the effect of any other mods you make.
