Looks like I didn't take of photo of the final roof prep. Like I said, I just chipped away a little more of the lap sealant, then sanded the dirty layer off, and cleaned everything. I'll be sure to let you know if it leaks
I set the fan back in the hole, and drilled pilot holes for the screws. Then I marked each corner on the roof with a sharpie, so when the butyl tape was in the way of being able to see those holes, I could still be sure things were lined up well enough. Then pulled it back out.
I put two layers of butyl tape on the underside of the fan flange, then set it down and centered it.
It seems silly to say but make sure that you set it so it's opening the right way! Unless you have a vent cover you shouldn't be driving with it open anyways, but if you forget to close it, at least this way the wind doesn't tear it off...
I started all the screws by hand, just to make sure everything went in nicely. The instructions say not to over tighten, but to tighten evenly. Makes sense. I wasn't sure how much to torque it...and since I don't really have a way to torque screws, I just used the setting on my drill. I started all the screws at 5, then took them all to 10, then called it "good enough" at around 12/13.
Two of the pilot holes either missed the wood frame, or somehow stripped out really easily. They wouldn't tighten down. I went back with the drill and put pilot holes in at an angle hoping something would grab there, and when I put the screws in this time, they did grab and tighten.
Trimmed up the excess butyl tape and called the roof "good" for now.