Once you set the TPS, try the “White Knob Method” to balance throttles....copied from an older tuning thread. This method is a quick way to get your bike running well without going too deep into the brambles:
Back off the RH throttle stop. Unless you have some super high mileage bike where everything is worn out and sloppy, using both will make you crazy.
Open bleeds one turn each. ("Micha's method") 1 turn is almost always right. Make sure the screws and ports are nice and clean.
Sync using white knob at idle. Like I said, some frown at this. Guess what? If they are synced at idle, it will be synced off idle.
When the throttles are open (>3k) the white knob needs to be moved a lot to make any difference in vacuum. This is because the small adjustments the white knob makes gets lost in the large flow of air coming through, and tiny imbalances in throttle vanes will be hard to see on any kind of meter, even the expensive one I bought.
You can turn the white knob and the throttles will appear to be in balance at higher RPM's. But they're not, which you will see when it drops to idle. Then you can use the bleeds to try to even it out, which is what I did, and then it idles worse than ever.
In short, the ultra tiny differences in throttle openings will be revealed at idle but will be lost at higher RPM's. If the idle is balanced, then higher RPM's will be balanced too.
Try "JB's" method, and sync the throttles at idle using the white knob. Turn 1/8 and blip throttle and let it settle. Keep doing this until it smooths out and is in balance. The idle will probably creep up as it smooths out (you can adjust this later using the LH throttle stop screw). It will never be perfect but you can get it close. Check "off idle" RPM's as you get it smoother, I bet they will be in sync too.
Yes, this method is backwards, but since your bike runs like crap right now, why not try it? I went through ever "method" before doing it this way, and now my bike runs like a sewing machine and pulls like a locomotive...