I also filled 2.9L This problem is also treated in this thread http://www.xt660.com/showthread.php?t=16450
I took out some oil without unscrew the drain bolts.
I used a water plastic bottle 0.5L with large cap.
On the cap of the bottle i drilled 2 holes. Though each hole i passed a transparent plastic tube ( 8mm) into the bottle. One of the two outside ends was placed in the oil filler hole and the other the other one was used to suck air out.
I took out aprox 300 ml considering the 0.5 L bottle used. I couldn’t find a syringe.
I ride it 60 km and than checked the oil level: bike straight up, waited 3 minutes (had to wait was leaking) , the cleaned dipstick inserted without screwing it, and the level seems to be at the max.

This oil level check seems like rocket science.