I was having problems with the 5D jig getting some lowers to put pins in the right locations. I finally measured the spacing between between the take down pins and had to turn the forward pin location around to get the pin locations correct. There was a .012 difference between there they were and where they should be.
Also, make sure that you mill the bottom of the well to the correct depth, I had to get a depth mic to make sure of this one. I didn't check this measurement on my first lower and had to cut it approximately 0.015" deeper to get the trigger to function correctly.
Also #2, lye (caustic soda) is your best bud.