Thanks for the tips.
I noticed that either the cowl hoop/brace is slightly off or the body has some irregularities. The hoop really wants to contact the drivers fender, and the pass side "foot" is not flat on the floor (about a 3/8 " gap between the bolt hole and the floor).
The braces to tie the hoop into the firewall were also a couple of inches off. They were nowhere near close, and I thought I might have the hoop positioned incorrectly but it's the only place where it can work with the door hinges lining up properly. The windshield brackets also collided and wouldn't fit until I slightly elongates the slots in the body and clearanced a section of the brackets.
Drilling/tap the doors was a bit nerve wracking but I think it came out well. I really took my time on that as I didn't want to punch through the door. I still need to adjust the hinges and plates to get the doors to line up better but it's awesome seeing it with the windshield and doors on. It's starting to look like a Cobra now! If the garage didn't look like it had been turned upside down and hit by a tornado I would have taken a picture.
Some other recent progress is that I have my steering plan figured out and mostly implemented. I had to use three universal joints and a single support bearing to make it from the rack, around the Coyote, and to the column. I thought I was going to have to use a double joint to make the bend around the valve cover but it looks like the regular single-joint flaming river part will make it without binding. These DOHC modulars are so wide! Before going with the Coyote I was originally going to go with either a FE or a SBF and every time I run into one of these clearance issues I keep asking myself why I didn't
Saltshaker, are you using a booster with your wilwood MC?