well sir, i'd feel like taking a match to that bike after the amount of money you have spent!
1. just read your whole thread, I've been there with my bike a few times. have you checked the coil?? I have seen those packing in, if you have access to a mates bike, steal his for a test to see if your own is working right
2. no matter how recent a plug is, they can foul, unless you put a new one in after this problem occured, did you??
3. you maybe have checked this, but i cracked a side casing once, oil from the gearbox seeped into the stator plate housing, leaking over the stator plate, and caused the bike to run like crap, if your crank seals were bad, your stator plate may have got a touch of gear oil, also check your crank cases for any cracks, as sucking in air would cause a bit of bogging, although you may have checked or noticed this when you rebuilt her.
the stator plate needs to be bone dry, when i raced my blaster with a bad crank case, each race i had to take the magneto off and dry any oil off the stator, just a thought
let us know how you get on!