I can't seem to get the needle it off the diaphragm to put a shim on it. Any tricks?

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If you are talking about the needle in the carbs; then once you remove the diaphragm, simply use a pair of needle-nose pliers to pull the white plug out of the slide, there is a spring in there followed by the needle and some metal and/or plastic washers.

Hmmm I tried.to.pull it.out but.it didnt want to.come out, and I didnt want to break anything.

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Use some wd40 or penetrating oil in the hole. Then get youe finger in and wiggle it and shake that white plastic plug ...
Watch out ... rant follows ...
And the freaking carb had a 1000 problems in the 89-00 bikes ... and the lack of plastic plug over the stupid needle was not one of them ... classic case of fixing what isn't broke, and ignoring what is well and truly broke,

Cool.
Buddha.

What does the shim do for the needle anyway?

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Quote from: Naemion on December 13, 2013, 11:54:16 AM
What does the shim do for the needle anyway?

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The tapered needle is raised/lowered by the movement of the slide; this lifts the needle out of the main jet allowing more fuel to be metered by the main jet (based on the area of the jet not blocked by the needle).

Adding a washer results in more of the main jet being open for the same slide position meaning a richer mixture.

The needle height mostly affects the Wide Open Throttle (WOT) performance through the mid-range of the RPMs.  I.E. if you go WOT at 4K RPM and feel a sudden jump in power around 7K rpm, then the mid-range is lean (wrt the top end) and you have to slightly raise the needle; conversely, if you feel a hole at 7K and then increasing again, then the mid-range is rich and you need to lower the needle.

When rejetting the carbs, you always want to start by finding the best main jet (best WOT pull at high RPMs).  Next adjust the needle height to tune the WOT performance in the mid-range.  Finally adjust the idle/low RPMs with the pilot jet, idle/mixture screws, and the starter/mid-main jet (on the 02+ carbs).