I finally got mine all installed, sorry for the late follow up. I found it necessary to cut my underbracing as well, per the original PMD directions. My pan actually made contact in the front right corner not allowing it to sit flush. Talk about nerve-racking, cutting on the hood. I used a dremel tool for this with a little cut-off wheel.
Once I could trial fit the hood pan I looked at the pan from the outside of the hood with the scoops removed and also at Colorado's pics (thanks) and decided to go ahead and glue the foam to the pan and reinstall. I too had to trim just a little bit of foam on the pass side just inside the scoop. Using a chip brush I dabbeded some flat black where I cut the foam and you couldn't tell a thing.
Both the upper and lower foam that came with the kit is a pretty dense foam. Since I am running a Torker II which is higher than the stock maanifold I had to do something different as that foam just did not allow the hood to close and sit properly. I installed the lower pan and placed 4 balls of aluminum foil where the foam goes. I learned that it is a slope from front to back with 3/8” at the front and 1” at the back. I ended up using some 1 ¼” strip foam from the hardware store that is much more forgiving and collapses easily. This worked great as the hood sits like it should and the R/A is completely sealed.
I then learned that the repop open scoops from PY did not fit right. The posts were located too far forward so the scoop wanted to set rearward, about 1/8”. So instead of hogging out the V slot in my hood where the posts fit I decided to open up my original scoop. That was a nerve-racking job as well as they were painted but the trusty dremel tool worked again.
This was all done in a thrash as I was prepping to go to the Pontiac Southern Nationals which I just made it. Judging place me in the 67-81 modified f-body class and I scored a bronze award. Lots of beautiful birds there and a few of the other first gens had ram air too!