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On my 99 EVO, I went from a 42 to a 45 pilot jet, and a 170 to 180 main jet. A little over two turns out on the idle mixture screw. That is with drag pipes and a K&N air cleaner. I was able to drop the bowl off the bottom of the carb without removing anything except the air cleaner and mounting plate along with the vent tubes that go to the rocker boxes. Just don't loose the jet needle guide when you drop out the main jet. Mine stayed in when I dropped out my main jet, but I think it is just loose in there. I do not have a crossover pipe on mine which I think made it easier.
When I ran a CV on my EVO I was running a 46 pilot and a 185 main. You can do it, its not hard. I suggest you replace any soft screws with stainless hex. Just don't get too tight.
I changed mine and my wifes A/C and exhaust's. Didn't have to re-jet, they run fine and plugs buring good, dealer says the carb's were set up on the fat side from the factory any way cause they know most people change someting right away.