If the pics you've posted show all of the problem areas, I think replacing the roof is a much bigger ordeal than patching the existing one.
But you need to get the glass out and get the metal wire-brushed (heavily?) to see what you have, before you decide which path.
As others have said, you need to see what the understructure looks like.
In some areas there are 3 layers of metal welded together (keep that in mind for later).
Right now, everything fits and is in spec and all reference points are intact.
For replacing the roof - are we doing just the skin? If so, there's likely 100 spotwelds that need drilled on the donor. That's not trivial. You could air-chisel or use a diegrinder on the receiver car. And again, sometimes 3 layers to deal with if swapping roofs.
If you replace the whole roof, there is potential to get it slightly out of location, such that F&R glass doesn't fit properly and side glass doesn't seal well. All measurements must be done *before* you cut the roof off your car, too. There's no going back to check something you forgot.
Consider the linear inches of weld you'll be doing. With patches, it's just that perimeter of each patch. Yes, your patches will be larger than the holes when you cut to clean metal. But if replacing the whole roof, you are now welding significantly more - more warpage?
IMO you'll possibly need more metalworking skills to replace it than to repair it.
There are rear window corner patches for B-bodies at AutoMetalDirect (AMD). They surely aren't a direct fit, but they might be helpful in the corners. (look at all the rear glass patches they offer, too)
And, nobody has mentioned the cost of a donor roof. And - shipping a roof is truck freight, or Greyhound or Fastenal, and it's on an oversized skid. That won't be cheap, either.
They will also cut it thru the pillars - you'll be doing all the spotweld cleanup at your house.
