As it turns out, i must of gotten lucky when Van's sent me the original material. I was going to order more but I decided to see just how much was left over from the original shipment. Turns out it was just enough to redo by a quarter inch.
I only had to move it back in the flat middle section. Each curved side fit fine.
I had same thing first time I closed the canopy after placing that seal. I tried tucking it in as I was closing the canopy, had a friend with a plastic squeegee-type thing push it an as we closed canopy. After sitting closed for a while, It seems to remain where it needs to now. Will keep an eye on it, but it seems to work fine for now.