To take the pilot jet out, you just use a small flat head and turn it counter clockwise. Maybe consider cleaning the whole carb out though? Take that out, the main jet, take the floats off/adjust, and clean everything. Blow the passages all out with compressed air, etc.
If it is lean, it will ping/detonate a little bit under loads, run hot, and sometimes idle a little high.
Before you get to far into it though, make sure the boot from the carb to the reem cage is not dryrotted, and the gasket around the reed cage, cylinder base too. Spray them with starting fluid with the engine running and the RPM's will change if there is a leak.
You might not have to play with the carb as much as you think. Clean it out good first... Also you said about changing the main jet, that primarily deals with the air fuel metering from 3/4 to wide open throttle. To test this, you need to wind the bike out in a higher gear 4th/5th with a fresh spark plug. As you near redline, Kill Switch & Clutch. Coast to a stop. Remove the spark plug. Take a look at the porcelin below the electrode. If its black/sooty looking you are too rich. White/white specks, signs of detonation, indicates a lean mixture. Should have a mild brown coloration to it.
Good luck with it.