Although all the jets work in concert with each other across the full spectrum, the main jet will have very little to do with your down-low pilot mixture, just as the pilot jet will have very little to do with full-tilt-boogie main jet operation. And since that's where you seem to have the issue (hell, it could be something entirely different going on, but one must start somewhere) I think I would mess with the pilot jet first, then proceed to tune the jet needle/needle jet/main jet - in that sequence.
I agree with you that the main jet will have no effect at idle or low speeds.
The pilot jet however, feeds in front of the slide at all times and therefore it could have a dangerous effect if your main jet was borderline lean and you installed a smaller pilot jet. It's always best to get the pilot jet sorted out first.
You'll know the pilot jet is correct when the air screw causes the engine to quit at about a 1/2 turn out or starts to stumble at 2-1/2 turns out. The ideal adjustment range would be between 1 to 2 turns out.
If the motor continues to run fairly smooth at a 1/2 turn out the pilot is to small. If the motor keeps building revs past 2-1/2 turns out, the pilot is to big. Make sure to reduce the idle speed as you open the air screw and rev's increase.
The next step I would do would be to remove the main jet entirely, drop the needle all the way down and make sure the bike blubbers at 3/4 to full throttle. Once you've done that, put the needle clip back in the middle position and then you can safely seek out the main jet.
If the needle jet and needle profile aren't allowing sufficient fuel flow, it won't matter how big the main jet is, because it's already being restricted in the needle jet/needle combo.
Trust me, this was an expensive lesson to learn. Half a dozen bigger main jets and then a fresh bore and a new piston, before I realized I had a restriction problem in the needle jet/needle combo.
The slide cutaway and the needle jet/needle combo control the transition from closed (idle) to approx. 3/4 throttle and should be addressed individually by plug readings at a constant 1/4, 1/2 and 3/4 throttle position. Sometimes a needle that gives a good plug reading at 1/4 throttle can go rich or lean at 1/2 or 3/4 throttle and a needle with a different profile in these area is needed.
It is also critical that the floats are set properly and the petcock is flowing adequate fuel to the carb.