I have never been able to get a good bleed on a bike with a vacuum system.
One of the best modifications to make bleeding brakes easy is a set of SpeedBleeders -
Speed Bleeder Bleeding Brakes Bleeding Motorcycle Brakes Automotive Bleeder Screw Brake Bleeder and a length of clear hose.
These make bleeding brakes a one man operation. Simply open the bleeder, pump the brakes while watching the fluid level in the reservoir, then close the bleeder.
Also while you are at it, look at the differences in brake fluids. The R3 can push the limits of some fluids simply because the bike can make prodigious amounts of torque and acceleration, and the weight of the bike and rider can lead to the brake system being pushed to its limits.
Brake fluids are not the same. And the humidity of the climate you live in plays a big part in how often you need to replace it.
Castrol SRF is fantastic, but expensive.
Motul 600 is very good and can be found online or at most bike and speed shops for cars.
Valvoline Synpower is commonly available, relatively cheap, and still works very well. But may require more frequent replacement in humid climates.
I wouldn't recommend anything lower on the list below:
Fluid------------------------------------------Dry BP-----Wet BP----Aprox. BP after 6 months (rough estimate)
Castrol SRF.............................................590 .......518.........554
NEO Super DOT .....................................585 ........421 .......503
Motul Racing 600 ..................................585 ........421 ........503
Motul DOT 5.1 .......................................509 ........365 ........437
ATE Type 200/ATE Super Blue ...............536 ........392 ........464
Valvoline High Perf Synpower ...............503 ........343 ........423
ATE SL ...................................................500........329..........415
Castrol LMA ...........................................450 .......311 .........381
Gunk DOT 4 Brake Fluid..........................510 .......311 .........411
_______________________________________________________
DOT 5 Spec ...........................................500 .......346 .........423
DOT 4 Spec ...........................................446 .......311 .........379
DOT 3 Spec ...........................................401 .......284 .........343
I hope this helps.