Reinstalling Rear Deck Lid Hatch Anyone Have Tips on Proper Alignment?

I would disconnect the struts first as they will just make things harder. I do my deckled R&R solo, using a simple sling made up of two small but long tie down straps hooked to my gantry crane. If you google it, you will see others use boxes, or wood, and towels or other padding to hold the deck lid approximately in place, but open far enough to insert the mounting bolts. Lots of different ways it can be done.

Do you see small holes between the hinge mounting bolts? If your car has them, these are alignment holes into which you insert a suitable pin punch, small screwdriver, straight mechanics pick or what have you to get the alignment very close and perhaps spot on. My car has three alignment holes per side, not sure if that's normal or not. Getting those holes lined up while the mounting bolts are slightly snug gives me perfect fit on one side, and very close to perfect on the other.

I did have two guys help once, one on each side holding up the deck lid while I did the bolts and alignment but that was a circus, resulting in a paint chip on one edge of the roof near the hinge. For me it's better done solo.

 

I've done it twice solo. The key is to get the alignment hole plugged with something (I use a nail on both sides) and also to mark the position of the bolts around the outside of the bolt heads before removal. It's pretty easy when you use those references. But of course the lid is too heavy to handle with one person. I use ropes and ratcheting tie downs anchored in the garage rafters to hold the weight while I get the bolts and locating nails into position. And yes, absolutely do not try to do this with the struts connected!

 

It's a small hole about 1/8" in diameter, one on each hinge, located between the two bolts. If it's there, you can't miss it. BTW my car is a 328 and all 328s have them AFAIK. You didn't say what your car is but if it's a 308 maybe you don't have them.

 

My early '77 has 3 alignment holes on each hinge. Sounds like you have already taken the bonnet off but when you get it aligned to your liking, scribe marks around the hinges for the next time!

I think you will find that the body gaps will end up being a little larger than you expect by the time you get the 2 spoiler corners and the 2 buttress to roof points correct. At least that has been my experience.
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We did it with 3 , struts not attached and even then we had a smal chip on a corner....painted directly after

 

You can do it with just one guide tool, and most anything with a tapered point can work. Snug up the mounting bolts, but not fully tight, then insert the tool into each alignment hole in turn. Might take a couple three times to get all three on one side aligned, then tighten the moaning bolts.