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.
I used to be indecisive. Now I'm not sure. I feel like I am diagonally parked in a parallel universe. 1968 400 convertible (Scarlet) 1976 T/A - 455 LE (No Burt) 1976 T/A New baby, starting full restoration. 1968 350 - 4 speed 'vert - 400 clone (the Beast!) 1968 350 convertible - Wife's car now- 400 clone (Aleutian Blue) (Blue Angel) 2008 Durango - DD 2008 GXP - New one from NH is AWESOME! 2017 Durango Citadel - Modern is nice! HEMI is amazing! 1998 Silverado Z71 - Father-daughter project 1968 400 coupe - R/A clone (Blue Pearl) (sold) 1967 326 convertible - Sold 1980 T/A SE Bandit - Sold