Ok, so this took quite some time to figure out. It was very strange and we still don't know why it happened. My dad disassembled his hinges to put in the new reproduction retaining clips. This requires removing the pin from the upper and lower portion of the hinge. In theory when it all goes back together there should be no difference in the hinge.
What was happening is that when the hinge folds, the lock pin that protrudes from the hinge mechanism must neatly fold into the notch in the lower hinge. One the drivers side hinge of my dad's car this pin would hit and catch which prevented the hinge from completely folding.
I apologize for not posting a picture but my dad dissembled everything on me. We removed the trunk and deck on my dad's cabriolet to repaint the trim and fix some paint issues. This seems to have been a bad idea because we cannot get the trunk to fit anymore. I've spent way too much time squeezed in there loosening and tightening the hinge bolts
We are now thinking that the hinges may have something to do with the problem. The way they are mounted, they point straight down when the trunk is closed (I wish I could have posted a picture). This doesn't seem right.
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