The little nubs don't HAVE to be ground down, but it can make your life a bit easier. I found that by leaving them they add a bit more "friction" for the rubber gasket and keep the projector from spinning, later down the road. I also use JB weld on the big nut you cinch down to mount the projector, effectively locking it into place by "welding" it to the housing itself. With that done, I run silicone all the way around the nut making sure to seal that square hole (4 o'clock) in your picture.
For the wires you can either drill a small hole for them behind the projector as suggested above, or you can de-pin the plug and feed them through that square hole on the right of your picture (at about 4 o'clock). That's the approach I usually take. I'll feed those wires, and the brown/white wires for the hi/low function through there.
