To Start I would recommend that you get the air-box back to original.
A carb will normally have 4 jets all operating different stages of acceleration.
1 - Idle Jet
2 - primary jet - operate when of idle to roughly about 4000rpm
3 - Needle jet + Needle - from 4000rpm to full throttle
4 - Main jet - This jet will only limit the fuel flow at full throttle and because one would only ever run your vehicle at full throttle all the time in racing conditions, this jet will have almost no influence on the carbs performance in normal riding conditions.

The idling jet will have little effect, but there would be no sense in changing this jet so I am sure it will be standard.
On the F650 Carb I do not see a primary jet so I would assume that the next stage will be the Nozzle needle and needle jet. Again there don't seem to be a needle jet but it seem as if the venturi is doing the jetting in this case.
I am sure the jetting problem will be between these two parts that will have to be replaced as a pair and because of the dual carb arrangement it will mean you need two sets.
Part number for the Nozzle Needle - 13 11 2 343 397
Part number for the Venturi - 13 11 2 343 395
Main jet - 13 11 2 343 396
Because I have never worked on this carb before I would recommend that you double check the info.
The idea is just that in most cases only the main jets are changed which hardly make a difference unless if your are constantly racing around at full throttle.
The mixture can also be regulated normally by adjusting the needle position up or down.