I had a similar situation and here is what worked for me;
remove the lifter shocks from the deck-lid
remove the lower catch assembly
loosen the hinge attachments
remove the rubber bump stops
remove any washers and or spacers in between the hinges and the deck-lid
carefully lower the lid
eyeball the lid from several angles to determine what needs adjustment
install the rubber bump stops and adjust
lower the lid again and check
tighten the hinge mounts
lower lid and determine if spacer washers may be needed.
adjust as necessary and tighten
if everything lines up at this point you should be able to attach the lifters
check to ensure the lid closes correctly and then attach the latch and adjust as necessary
Like I said this worked for me, hope it works for yo as well.
Beer helps, good luck
