On flipping the MDF:
Since I use qwas dogs as my fence, I expect I may have to recalibrate slighty when flipping. But at that point, I should be able to quickly calibrate since all the kinks will have been ironed out (toe-out, bevel, etc.)
On stop screws:
See picture attached. I mean the stop screws. Basically, they set your 0 degree angle. I think the back one was not perfectly set with the front one. Here's my procedure:
1. Take 2x6 and joint face
2. Plane other face (both faces now parallel)
3. Cut on MFT, check square of cut
4. Adjust back screw until square
5. When I find a zone where I'm either slightly off inwards, or outwards, tweak SLIGHTLY front screw.
6. Repeat until I get a square cut.
Using this procedure, I've gotten a pretty good result.
As for toe-out, that was it. I've no longer those awful marks and squaring my table has become FAR easier:
1. Place dogs parallel to guide rail on the left column of holes closest to the rail
2. Place the fence rail that comes with the MF3 between dogs and guide rail
3. Press firmly guide rail against fence rail, clamp guide rail holders in place
4. do a test cut, check for square
5. if not square, move the bottom guide rail holder until square (repeat 4-5 for 15 hours)
6. Adjust factory stops to match adjustment.