if you just change the main jets, you should not need to re-synch the carbs. this is not affected by changing the jets. if you're sure you got it synched right already, you can leave it alone.
when you say you raised the needle clips one notch, do you mean that you moved the clips from the middle to the second from the top notch, or did you move it to the second from the bottom? to raise the needle, you need to move the clip down to the second from the bottom notch. just trying to cllarify, cause i couldnt tell from how it was worded, and it can be confusing.
as far as the pilot jets go, i have 2 bikes running stock 40 pilots. they run fine with no issues with teh mixture set at stock, or vey close to it. one bike has unbaffled 4-1, pods, and 125 mains. needle in second from bottom notch. the other has unbaffled drag pipes, pods, 120 mains, needle in second from bottom notch.