Just got paint and body work finished and now im adding all the little things like new handles, emblems, etc. My new rubber stops came in from inline-tube and trunk lid wont shut. I pushed down on it pretty good but still wont drop down where it should, Its an aftermarket lid so that may have something to do with it. I put my calipers on them and they measured about .360 thousands. Just wondering if anyone else has ran into this.

You sure it's not the trunk seal itself ? I bought a full kit that does the whole car. Door seals weatherstrips...etc
The trunk seal in the kit was way to thick and I really had to slam the trunk for it to close and it sat higher when it was closed. I mentioned this to a friend of mine and he knew of the problem and he found me the correct trunk seal for firebirds. It is a different Extrusion than what's typically sold. The lip that seals to the deck lid is thinner.

Its not unusual that the trunk weatherstrip takes a bit to settle down (compress). Takes a few months of slamming the lid.

With that said, your post mentions the 'stops'. I typically have had to grind down the thickness of those too. So not sure which item is the issue.

And yes, a repop lid could be a third issue.

The stops on mine are about 1/4 in. They are not the originals but I replaced them many years ago.

Havent put weatherstripping in yet, guess I'll be grinding my down also.

I had the same issue. New stops and a reproduction lid. And like you, test fitted the stops before installing the seal to make sure it wasn’t the seal. The repro stops were the same thickness as yours. I cut them with a new SHARP razor knife then tested, then had to cut them down some more. They ended up being barely more than an eighth inch thick before the lid fit correctly. Then lightly ground them to smooth the cut edge.
Went with the SoftSeal hollow core trunk weather stripping, which worked well and threw away the one from Classic.

I had to shave a little off of mine too. Stock trunk lid.