I know you are planning to keep the patina. I like that idea and would do the same!!
What I would do about this alignment issue is take the entire front clip off and make sure the fenders, apron, grill, etc. are all as straight as possible. Then I would buy all new bolts for the front end, bushings for the radiator support and hood, etc. Put is all back together with all the bolts loose, get someone to help make sure everything is lined up, then tighten everything down. You may have to drill out a few holes in the fenders and use a few shims, maybe a ratchet strap or two to hold everything straight and to get everything to line up before you tighten it all down, but as you know, this is normal body panel alignment stuff. As long as the frame and tub are straight, the rest of the panels should be able to be lined up pretty straight.
While I had the front clip off, I would take the opportunity to address some maintenance and reliability issues. I would clean up the engine, firewall, go through all the wiring (replace any old or crappy wiring), probably go ahead and replace the belts and hoses, etc. Maybe do a little detailing under the hood and the back of the fenders. You don't have to paint anything, but you can seal any rust areas with a rust converter. I recently bought some Corroseal rust converter for my FJ40 and put a little on the frame and rusty part of the fenders on my FJ55 just to see what it looks like and it looks good. It dried sort of a dark rust color (very patina like) and should keep the rust from continuing for the next couple years.
MM