From your description, I would guess your problem is with the pilot circuitry--not the needles or main jets. If you did put 42 pilot jets in the carbs, you will likely need to turn the pilot screws in to lean the mixture some. My 790 has 42 pilots and the screws are only out about a turn. Having said all that, I did have the screws out about 3.5 turns before I got it on a dyno, and it ran good. If you still have the stock 40 pilot jets, you will likely have to turn the pilot screws out some to richen the mixture. You might want to recheck everything done in and around the carbs...look for vacuum leaks...make sure the vacuum nipples are all on, etc.
I know nothing about the TOR's, but I wouldn't be surprised if the 150 mains are a tad rich with the TOR's. However, all bikes are a little different, and my OLD butt dyno is not sensitive enough to get the mixtures at optimum--only a good dyno with EGA. :-D
'03 T-100: Nark, NH Togas, 158 mains, 42 pilots, stock needles--no shims...dyno'ed at 745 ft. elevation.
Larry
edit: Just reread your post...what does "breaks up at 6000 rpm" mean? At that rpm you should be running mostly on the main jets--that is the rpm that mine really turns on--like it is lifting the front wheel off the ground. When I had too small main jets in, mine ran about like stock--but no stumbling or anything like that. The largest size main jets I have run were 160 and I couldn't tell a difference between them and the 158's the dyno run liked the most. The old rule of thumb is to get the main jets sized correctly first; second, get the needles correct; and last do the pilot (idle) mixtures.
I started my jetting with 135 mains and Thrux needles, and like I said it ran about like stock until I put in the 150 mains.
[ This message was edited by: RedBird on 2007-01-04 20:17 ]