1) Do the stock fuel lines need to be equal length? My left side (Choke side) fuel line is like 2", while the right is about 4"
doesnt matter
2) In general, how does my jetting sound? It's only getting colder around here..
main not to bad where its getting cooler. So im guessing you have toomey needles? six clips instead of five? keep an eye out for stock needles toomey ones suck, but not bad. pilot is way to big id try a 27.5 see if it clears up maybe even a stock 25.
3) I accidentally rode it lightly not knowing the idle screws weren't included, and the bottom end felt like garbage- will properly set idle screws avoid this air leak and allow me to continue tuning?
yes i didnt have idle screws on my bike first few months i had it when i didnt know any better
4) What jets control from idle to about 1/2 throttle? That's where it feels as if it's breaking up, but after that, it pulls HARD.
pilot, a/f screw, and needle
5) Any other quick mods/precautions I should take?
Getting your crank welded would be my first suggest then cool head to bump comp. and some porting when ya wanna go faster.