I had this exact issue on my 70 Bee. It made the lid sit high at the back and it looked terrible. I could not do anything to make it go away. I searched around and found a really soft gasket. That made the problem go away. I can't recall which brand I used...maybe Metro? As I recall, I had two different brands on hand and used the one which felt the squishiest. I recall for sure that the rock hard gasket came from Year One.
I had the same issue on my doors. The new rubber was so damn rigid that you really had to slam the door so hard, you thought the glass would shatter. Left it in the sun with door closed, etc. but no help. Again, found a softer gasket that made all the difference.