How did you get the fit right? You can't hold the rubber/clamping strip in place while it's fitted, and then drilled.
I did pretty much what Paul described- I got the fit between the cowl and baffle ramp where I wanted it first. What follows might be called historical fiction
I don't remember the precise details of how I did things, but this is pretty close.
The seal material is around 1/16" thick (don't quote me on that). I found a rectangular piece of aluminum about the same thickness in my (very large) scrap pile- I'd guess around 1" wide by, oh, 4" long. Laid that on the baffle ramp with cowl in place and attempted to slide it forward under the cowl lip. Continued messing with the baffle till the test strip just slid under the cowl everywhere I planned to have rubber.
With the cowl off, I cut the rubber to length, then made the aluminum reinforcement strip, then marked on the cowl where I wanted the holes. I have enough Pony spring clamps left from my Sikaflex canopy project to supply every hardware store in the area, so I used a few small ones to hold everything on while I drilled the holes. Knowing me I probably used a #40 drill at first, in case I needed to move a hole a teeny bit (unlikely here, but you never know). What I do remember clearly is that when I opened the holes up to fit the screws, I made the holes in the rubber substantially oversize so I could pull and tug on the rubber to get it "just right" before final tightening.
As for Paul's mention of potential heating issues due to leaks, that was my motivation for trying to get this right. I've read enough about heating issues that I figured I'd get my baffles well-sealed up front. Summer temps here routinely top 100? F, so I don't want to give away any performance.