You spent $20 to get the sprocket fitted to your hub and it's still not aligned properly? I'd ask for my money back
Anyway, I would pull the motor and sprocket off the bike, and start over again. Get some somewhat decent instructions (I think livefastmotors and thatsdax have decent instructions).
Head down to Ace Hardware and pick up some M6x1.0 allthread since you said you broke some mount studs. Not sure what grade they have, but it's gotta be better than the stock junk. (they carry short lengths, like 4" or so) Not sure, but their service desk may even be able to assist you in getting the busted studs out if you can't do it.
As for the sprocket being misaligned, have you tried it facing the other way? Most of the sprockets have a bevel to them, and it can make a difference.
The clinking sound, no way for us to know unless we heard it I think. I would pull the head and slowly rotate the motor via a big screwdriver in the small sprocket on the clutch side and see if it's anything internal. Then put the head back on torqued properly, make sure the plug is torqued as well, and go from there.
The carb...there's no way a liberal amount of silicone shouldn't do the trick (just don't get it inside the intake.
I'm in Longmont, but I work 6 days a week (at work right now), and only have 1 car between my wife and I, so I don't have much opportunity to go anywhere.