Troy, did you get a new nut for the cdi? You have to replace the novi with a differnt stupid special nut and make sure you get the correct thread pitch and direction for the crank you got. Also, the woodruff key on that crank cdi combo lines up perfectly for 1.5mm btdc and makes timing stupid easy. You can run the stock head, all the aftermarket options put your compression over 200psi and really fuck shit up. I think you got basically everything, I would probably replace the motor mounts and brakes too.
Jbot, he has a sim hi-flow moby pipe and it actually scoots pretty good in the hi rpms.
I'm gonna say dont do the clackmaster er2/3. it is a fucking pain in the dick unless you rig up a pull start or spend $$$ on a kickstart unit. The stock variator is fine with kitted and mild piped bikes, it is moderately tunable if you get a 4 ball guide and actually tuneable if you get a varplus. I usually don't bother with the varplus because it requires removing several annoying circlips.