As far as the right angle guide, everyone may be overthinking it a bit. I just draw a 90 degree angle with the polyline tool - the software shows when they are at 90 degrees. Then the dogbone fillet and an Inside/Left profile on it.
Cutting too shallow - you said you mic'ed the material, but have you ever Mic'ed your ZZero plate? Mine was off from the default, 0.121", so had set the actual thickness in the SB3 software. You should not have to keep going deeper to get to where you told it initially. I regularly leave 0.002" skin on the bottom of my material for cutout passes, to avoid using tabs or cutting into my spoilboard. (When doing this, I ZZero to the table)