lizrdbrth gave this answer and I'm gonna address them one by one the best I can
"Your situarion is a bit unique. It might pay you to get your hands on a stock TW and ride it to get feel for whether what you consider "twitchiness" is normal, the result of nearly twice the horsepower or caused by mechanical issues.
"Twitchy" being subjective, TW's are twitchy. A bit oversprung in the rear, and a 52 inch wheelbase is a 52 inch wheelbase. Add enough power to easily loft a front wheel and those alone could cause what you describe as "twitchiness". Just for comparison, the bike your motor came out of has 6 more inches of wheelbase. A hyperextended swingarm will put more weight on the front end.
If the excess power is causing thr front end to lighten up lowering the rear may make things worse. Under power even more weight may be transfered rearward. Think "60's Gasser".
But lowering the rear or lifting the front will definitely slow down the steering. Drnlling the swingarm shock pivot is a reversible mod. Just don't get carried away because a 3/4" difference does not equal 3/4" of lowering, but more on the order of 3".
The other option is lifting the front. YZ80 fork tubes will allow a little over 2" more height.
Proper fork oil level will help keep the forks from unloading as easily. Or at least more predictably. A few less teeth on the rear sprocket might dumb down the tendency, as well.
If you mean "twitchy" at a given speed (like a high speed wobble) that indicates a mechanical issue.
High speed wobble indicates loose or worn steering bearings or swingarm bushings, misaligned tires due to uneven snail adjusters or front ubes twisted in the triples, tire balance, wheel bearings, low or high fork oil, etc.
Your bike has a fair amount more power. If it's worn swingarm bushings every time you twist on it your bike will tend to react more violently than a stocker, even at relatively low speeds. The swingarm will cock sideways under torque. When you back out of it or clutch to shift gears it will unload and cock the other way. Tail wagging the dog.
Your bike has had a fair amount of frame modification. While it looks great and appears to have been done properly there's always the possibilty that the frame has a bit of misalignment. If you can't cure the twitchiness through handling adjustments I'd take a more critical look into that possibility. Even one degree from vertical on the steering head will give you issues you'll never sort out.
Have you ever ridden a stock TW?"
I'll do my best to answer here.
#1 yes I think a longer swingarm will help a lot. I'm speaking with Trickstr about his extended swinger.
#2 yes I think this is a direct result of added power, at speed it settles down somewhat.. under hard acceleration it gets a little squirrly
#3 I will look into drilling a new lower shock mount hole, this is reversible easily.. I like that idea
#4 I'm looking into another set of forks right now
(does anyone know the length of inverted KX100 forks?)
#5 ya know... I counted the teeth on my sprocket and I'll be damned if I can remember how many (raining now.. will check later)
#6 the po/builder was meticulous with this build, ALL bearings and "wearable" items were replaced with new, as mentioned the problem shows up under hard power and settles down once you back off a little and aren't actively accelerating.
#7 nope, I've never ridden a stock TW