I only have experience with 1.75mm filament and a Bowden tube. I would expect it would take a lot more force to push 3mm filament through a tube, so you might have problems with the extruder. Perhaps there are others who have tried 3mm who can speak up.
As to the controller, pretty much any controller should work. I've designed the mounts specifically for a Printrboard, so I don't know how well they might work with other boards.
As to the controller, pretty much any controller should work. I've designed the mounts specifically for a Printrboard, so I don't know how well they might work with other boards.