Runs absolutely perfect then wont start

[TwoManyXS1Bs]

... When it fires lights are bright right from the kick. When it won't fire headlight is dim almost nothing...

That's a clue.

...Another thing that's confusing is why it will not start until I put a battery to it but if I immediately hook the cap back up its fine with the fucked uP cap. That just doesn't make sense to me...

This probably won't make much sense either, but I'm thinking regulator.

There's an obscure phenomenon that can occur within MOSfet devices, that defy normal logic.
Hard to explain, but it *could* have the reg locked into shunt mode, dumping the PMA's current, even though the system voltage tells it to provide charging. Then, when a battery is hooked-up, the MOSfet circuit resets/unlocks, and returns to normal. This regulator may be sensitive to some 'normally-tolerable' line noise (back EMF?), and enters this fault state, until reset with battery voltage. This would be caused by one of those 'roll-of-the-dice' scenarios at the moment of 'ignition off', when the PMA is still producing output at some point in its phase, ignition may be firing, and the 'switched hot' part of the electrical system is now floating, absorbing all this, and exposing the reg's voltage sense to it.

Clear as mud?

 

[sickofitall]

Uh yeah..... it's all very confusing to me. This would be a lot easier for me if it was just something mechanical. I gotta get this figured out because I love this lil bike. I ride it all the time and this is really making me upset. It's been so reliable up until now it's driving me crazy. What you just posted TooMany makes some sense to me. I have another reg/rec around here somewhere. I'll have to try that as well.