In terms of getting the headlight to be flush, as in "retracts to closed position too much" or "does not retract down far enough in close position," I thought you adjusted it via the screw you may be referring to. Here's several pics I quickly found while I stripped my car down. I have a ton of pics regarding this whole area and assembly, if you want more.
The adjustment you are referring to I believe is for the cosmetic headlight cover piece (the painted part of the headlight) to properly align the gaps around the hood, but not sure if that actually deals with the up and down flush alignment with the hood.
I could be completely wrong, I'm just going off what makes sense in my head w/o delving into it too much.
Bryan