Ok guys I have a little update for you, I worked long into the night, and got the notches within an 1/8 of an inch of being parallel of each other measuring from the side to the back of the frame, but they where dead on square. This morning I pm'd Nate at Porter Built to see if he had any insight on my conundrum.. He assured me that an 1/8" was well within tolerance and that I could move forward with out worry. Thank you guys for all the suggestions, links and words of encouragement.. Also thanks to Nate for helping with everything its nice to have a company that stands behind and offers great support for there products!
Now as soon as I get done with this pesky thing called work, I can get back home and finish my notches..