Couple of lessons learned since this got tagged.
I got the doors hung to include the strut, but then gapped one door with the strut off (thankfully I started with one door at a time). Then I sanded the gap (I use a hotel key card with 40 grit, but start with 120 single side, then double it over, then got to 80, then double over 80, then 40 grit with the card, and finally 40 grit doubled over made for just about a 1/8" gap). I measure my gap with two tongue depressors glued together.
Then I decided to make the door even with the canopy (they were close but needed some glass work). So on one door I used some 1/8" door gasket in the gap, someone else on here had done it. I put the gasket on the lip, and put packing tape on it so the epoxy wouldn't stick, put the door on (without the strut installed, big mistake). I built up the areas that were low. After it dried, I got the door separated, reinstalled the strut, and it did not line up at all and the gap was way off. DON'T DO IT THIS WAY, better method below.
So since I was nearly starting over I decided to try a different method. First, everything needs to be on the door, to include the strut, all of the door mechanisms, etc. This is probably obvious to many, I should have know better. Next, I used packing tape to keep the doors from being epoxied together. I used sections of tape and overlaid one piece on top of another (sticky sides together, with about 1/3 of the sticky still exposed). Then I stuck the tape to the door sill, which resulted in none-sticky exposed above the door when the door was closed. Then I built up the low areas (and had to rebuild some of the gap, since it wasn't even). Once I was satisfied that my door canopy interface was level, I gapped the doors like I did before. Gapping was quick, maybe a couple hours; getting the surfaces level took a few build ups.