P.O hacked up my inner fenders need repair ideas

I am editing my reply because I didn't read your question close enough the first time and now realize you want to keep the fenderwell headers. Don't know why but I thought you wanted to make it back original.

If you want to keep them you don't have much of a choice I don't think. They pretty much need that much fenderwell cut out for clearance. Although I will say the PO did a hack and torch job on it that could have looked alot better. If you don't allready have frame connectors I highly suggest them since they took out some body strength by cutting the inner fenders away.

You can make some sheet metal plates to slip in to cover up the holes better than they are and make them removeable by sheet metal screws. That's about all I can think of.