Hey Trike Builder,
From some of the posts I've been reading regarding the jet size/ needle position, it would seem that most bikes out there are running really rich. Normally you have to go one jet larger than stock when running headers because the headers free flow more than stock but also the design of the header will cause a negative back pressure pulse in the pipe sucking more exhaust out of the cylinder which also make the valve overlap more effective. This effect tends to cause the mixture load in the cylinder to be slightly lean and therefore you usually have to go one size up on the main jet.
Normally, one would select the main jet based on full open throttle performance. Ideally you would determine this on a dinomometer. Once the correct main has been determined, you start adjusting the main needle to properly blend in the part throttle metering.
In the old days a header manufacturer would suggest that you start with a certain size main primarily to protect their name. No one wanted to be known for blowing up engines because of their headers, but there are a lot of factors which need to be considered when jetting. Compression ratio and camshaft duration are usually the primary considerations.
For those who have never come across this document it's excellent reading on selecting carbs and setting up. Most of what I'm stating here is based on my reading/understanding of the fundamentals in this document produce by Mikuni carbs.
www.mikuni.com/pdf/vmmanual.pdf
Another great read is a book called "Scientific design of Exhaust and Intake Systems" by Phillip H. Smith which is a Robert Bently Automotive Publishers book last reprint according to my copy was 1998.
I'm a motor head, what can I tell you. I've been reading this kind of stuff ever since I first smelled Klotz racing fuel and I can tell you that was a loooooooooooooooong time ago.
Enjoy
Kawboy