One of the struts was stuck so I tried some oil and pulled up. Did not work. I removed the strut and replaced it with a new one. Now there is a fairly large gap and the rear hatch / liftgate will not line up and close.
Do you think the hinges were bent? Any ideas on where to go from here?
Depends on how hard you pulled up on it trying to get it open. It is possible you bent the hinge. I would look there and also make sure you got the right length struts. If the new ones are too long you will have problems.
I've also heard of people intalling them upside down. But I;ve never actuall seen it so that one is just hearsay.