My initial problem was that the bottom of the hatch was off to the left, so it wouldn't latch. I figured I would just loosen a few bolts and bring it back around. I ended up getting in all kinds of trouble with the top of the hatch catching the roofline, latches not unlatching, and time running out as I really needed the hatch to function for the rest of what I had planned that day.
I eventually got it back to the way it was, just misaligned at the bottom left. Then, I am not proud to say, I took a 10 foot pipe and pried the hatch until it lined up correctly. I'm a procedures guy, but at least it works now. The hatch is still running high by about 1/2" but I may have bent up the upper lip of the hatch, and I may continue my Flintstone repair methods with a rubber mallet. My latching isn't that great but my striker pins are in pretty bad shape. I'll replace those next week and see what happens.