The quarters having been replaced without knowing what structural damage there is from the hit makes the situation more difficult and...What kind of work did you do to get "more adjustment" from your sub-frame? Things appear to be adding up as to why the front sheet metal doesn't line up.
When restoring a vehicle, certain procedures need to be followed, (You don't install the windshield wipers without a windshield being in first, I'm sorry if that sounds obvious but it's a fact and I'm not trying to be nasty), even more so on a Uni-body car like your Nova where you don't have a 1 piece frame and in effect, the body becomes part of the frame. Couple that with it being involved in an accident prior to the restoration.
This might help everybody involved and yourself...do you have pictures of the car the day you bought it or just before you started restoring it, all in one piece with smashed fenders and all so we can see what we are dealing with prior? Right now with the information coming in slowly and us not being there it's very difficult.