My words were not clear so I went to my car for a pic. This is the striker. It controls the position of the rear of the deck lid-
One bolt is visible here, the others are behind the bumper. Car doesn't have a sill plate, just the trunk carpet so woops. Pull the weatherstrip back a ways and work the carpet over the striker if you want to see it. Your new lid looks barely off side-to-side, so thats the part where I suggest a 2x4 block against the striker then thumping the wood with a hammer. Or hitting the striker directly. Its probably sitting where it should be but just bent a little.
It is possible that the rubber screw in type bumpers on the lid are holding it up. If so, screw them in until it sits level. That should set the height unless the striker has moved upwards.
Is it hard to close? I'll check back after dark. Good luck.
