I rebuild carbs but I wouldn't be willing to do it because I can't tune the AFR without being at the bike with it running. With a 4 into 1 and the pods being the bigger issue for CV carbs, I couldn't adjust the AFR properly.
My bet is you have Mikuni BS34 carbs on the bike. True? That is what came on them stock.
Several things can cause the symptoms you describe. Daveo's comment about the mechanical advance could well be the issue. It is simple to remove, clean, lube and restore. It is something I do to every new bike I get as part of the initial maintenance. Did you check it?
It can be the carbs. You spoke about the plugs over the pilot jets. If you look down the opening for the main jet there is an opening near the top between the main jet and the pilot jet that allows it to operate. (looking at the main from the bottom turned over in your hand) What can often happen with those damnable pods is they don't create enough vacuum to life the sliders and pull the needles up further opening the main jet. It can also be a leak in the diaphragms on the sliders. TEST - Carbs out on the bench, ensure the choke plunger is closed, raise the slider and cover up the oblong port at the top of the intake bell with your thumb and release the slider. It should drop VERY slowly. If it doesn't you have a leak preventing the sliders from raising and pulling up the needles out of the main jet.
If the carbs on back on the bike, pull the pods off and see if they rise (should be fairly even) when you go past 4K to 4.5K rpms. Keep a fan blowing directly on the engine when you are running the bike in a stationary position.
This vid may help orient you as well.
These are not your carbs but it will give you a sense of what you should see if the sliders are operating properly.
If you give Daveo, me and others feedback on what you found when we ask you to check something, you'll get better help.