Some delete the overflow bottle. There would have been a hose from rad to bottle behind air box. Then another from bottle back to and up over steering hoop. Vent from trans goes over hoop also. Stock, it has vent from clutch cover T-eed in, tho some delete that also.
When you tear carbs back apart, clean them pussy clean. Set float level, start with air screw 1 1/2 turns out from lightly seated. Do you still have the TORS brick on top of carb? Is so, that is where the idle screw is, if not, it will be on sid eof carbs.
Go to FMF site and see if there are any recomendations on jetting. Kinda sounds lean, especially if you have aftermarket air cleaner or no air box lid.
BTW, you can sync carbs closer for now either by sight or feel. (that's all I do, lol)