Ok, I spent a good 3 hours today,off and on, disecting this. I think I have it licked. I should have it sewn in and finished tomorrow(hopefully).
I bought some 3m outdoor carpet tape and used it to hold the window in while I sew. I started with 3 stitched points to hold it in place and make sure I had it centered. I started at the top in the middle, then did the top two corners with one loop. I left the needles hanging with enough thread to get the the next starting point clockwise.
Observation, the 3m outdoor carpet tape I got is black and is really sticky. It is working like a charm and should help a lot with waterproofing.