I don't know if you got your answer yet. I know exactly what Eric is talking about, my body panel was mostly non existent, and had a fair share of abuse from the previous owner trying to shut the truck.

I took some pics of my set up, if you need bigger I can send the originals, just mail me.

If the latch, part on the deck lid, is not aligned, the lid could be bent. Not uncommon on rusted trunks. The striker can also get out of alignment as Eric said. You can pretty easily see how the contour and angles should be on the inner body panel stiffener it bolts to. We take hammers to these parts all the time to get them to "align" once wrecked. Metal fatigue and wear and tear can cause these parts to bend a bit over 40 years or so.

If you got someone small they can go in the trunk with a flash light and watch as the parts come together to see what is going on. I know it's damn near impossible to see the final latching with the way parts are tucked in there. It really shouldn't hit anything until the final mating about a half inch away from locked.