Copied from the xs11 list @ www.xs11.com This should give you an idea of which way to go in regard to different Intake Exhaust configurations.

Note:

This document is based on Mikuni Carburetors. But the theory follows through on all carburetors. Be aware that Mikuni Main jets increment in steps of 2.5, Hitachi Main jets increment in steps of 2.0. Hitachi Main jets (screw in style [Yamaha XJ's] are available in sizes from 110-134 in increments of 2.0. All this means that if you find you need to go up 4 steps on the main jets according to this chart (2.5x4) the step up would be 10.0. For Hitachi mains the step up would be 5 jet sizes (2.0x5) since following this chart for Hitachi mains would put you at 8.0 which is very close to 7.5 which would be 3 steps according to this chart. 

Jetting Recommendations
by Denny Zander

Here is a simple set of jetting guidelines that have worked for me. For those considering jet changes, this might help select a starting point.

1 jet size for custom 4 into 2 exhaust

2 jet sizes for 4 into 1 exhaust

1 jet size for K&N filter (single inside airbox)

1 jet size for drilling out the bottom of the airbox

2 jet sizes for both single K&N and drilled airbox

2 jet sizes for individual filters

2 jet sizes for no muffler (open header)

1 pilot jet size for every 3 main jet size increase

Add up all the jet size increases and subtract one. (Remember they go in steps of 2.5 for each jet size)

Under a mismatch condition, like individual filters and stock exhaust or 4 into 1 header with stock filter and air box, subtract an additional 1 jet size.

Check plug color often, sync carbs after each jet change, make sure the floats are set correctly, and seriously consider purchasing a Color Tune. (See "Color tuning Carburetors" in the Maintenance Section).

Make sure your carbs are in perfect working order before making jet changes.

Example from my '79 XS1100 F:
Stock main jets: 137.5

Stock pilot jets: 42.5

2 sizes for 4:1 exhaust (Jardine)

1 size for single K&N

1 size for drilled air box

4 (main sizes) - 1 = 3 or 137.5 + (2.5 * 3) = 145.0
1 (pilot jet size) or 42.5 + (2.5 * 1) = 45.0

With this jet configuration I get 32-38 mpg on the open road, Smooth idle, very strong acceleration from off idle to 80+ mph, and steady pull past 120 mph. My "F" has 65K mile on it, of which I have put 33K with this jet configuration.

Happy Jetting

Additional info: Decrease main jet size one step per 2000' above sea level. Decrease pilot jet every 6000' above sea level.