well, my problem was actually quite different in that it was running fine, just not producing much power above 10K rpm in 5th and 6th gear. That was a horsepower problem -- my main was too small and just wouldn't pull anymore.
My problem was solved by going from a 97.5 main to a 105 main. I may still go up to a 107.5 as I was getting some popping today when under hard deceleration down from the redline. Didn't get to check my top end yet, but she was pulling real good still at 100. Also, I synched up the float levels, which were a little off, and I replaced the emulsion tubes, which were worn. now she's SWEET!
To check the main jet size, you have to pull the carbs, drain the float bowls, take them off and look at the jet (brass thing in the middle). It will have a number on it. Check the factory specs (in the service manual) for the stock jet size and compare to what you've got. They move, afaik, in sizes by 2.5 increments with a bigger number being a bigger opening and more gas!! woot!
To check the needle position, pull the top caps off the carbs (watch those little o-rings!!!) and pop the slides out, pull the needles from the slides and look at them. If they have more than one groove to hold the clip, they are aftermarket needles (one groove is stock). Count the clip position from the top and that gives you the needle position.
I would guess that with a full yosh pipe, you should go up 1 or 2 jet sizes on the main and MAY have to adjust the needles as well. Higher numbers for needle setting are richer, lower numbers are leaner. If you have a stock carb setup then you are most likely running lean, but in my experience, stumbling is more of a rich problem than a lean problem. ymmv.
the best way I know to check main jet size is do some top end runs (be safe!) and use the jet that provides the highest top speed, in otherwise similar conditions (same road, same weather etc). When you've got the jet right, it will be the fastest, go up one too many and she'll slow down again.
you should read this:
http://www.factorypro.com/tech_tuning_procedures/tuning_carbtune,CV,high_rpm_engines.htmlits hugely helpful. As is the whole factory pro site. check it out.