As I recall besides the adjustment on the loop on the hatch lid, the lock mechanism on the body is also adjustable, and you may need to play with that.

I also have a little bit of news you likely won't want to hear. The II's are a uni-body car and have a very bad habit of the body twisting under hard acceleration. The hatchback cars have even been know to blow the back window out while dragracing. The worst cars for body flex were the T-Top cars and to help eliminate the flex on these Ford added engine compartment braces which I noticed in your before and after pictures of your engine compartment were missing. As the body keeps twisting your going to find the doors and the hatch will need constant adjustment.

If you haven't already, at a minimum you should replace or build a set of the engine compartment braces and add a set of sub-frame connectors. Ideally a 6 or 8 point cage could be built to virtually eliminate any body flex (it will also help the car hook up a lot better.