does it idle at all, have you tryed to adjust the idle screws? what are your air screws set at. your mains should be in the 280-300 range with the lid on and 300-320 range with lid off, your stock pilots should be fine there 25's.
usually when a engine is hard to start cold it's due to lack of fuel if everything else is working properly. is your choke working properly, what size pilot are you using, what is your air screw set at.
if your oil level is to high it will leak out of that hose. the trans takes 1.6 quarts.
you don't need the overflow if you keep your eye on the coolant level
you didn't describe how it was running, but i'm gog to guess lean. you might ge away with the 280 mains with a stock air box, but with dual k&n filters i would try something in the 310- 330 range, with the clip in the forth spot from top. good luck
make sure you have a good connection at the coil, check spark plug caps, is your tors still hooked up, if it is check the throttle switch, carb switches, make sure you have a good ground.
I have t-6s also, but the fact is toomey designed them for a stock port motor. they respond well to bolt on mods, but toomey themselves will tell you to run the t-5s if your going to port the motor
the cushions under the basket are wore, that doesn't cause to much trouble. it's where the tabs on the clutch plates rub on the fingers in the basket that will cause you trouble,if there grooved up.