After the rough trim last night, I was able to put the cowl top on, but I still needed to get the right clearance between the baffle and the top… about 1/4″. To do this, I used the paper clip method. Basically, you put a ton a paper clips on the top edge of the baffle sticking up about 1/2″.
Then you put the cowl top on.
The paper clips will have been pushed down and will still be sticking by the amount of gap you have. You can then measure down 1/4″ (the desired gap) from the top of the clips, make a mark on the baffle, and then trim down to those marks. Rinse and repeat.
After a few iterations, I got a pretty consistent gap.