I knew that this 4runner in particular had been in an accident or two. The two that did the most damage being:

(1): The front passenger side wheel was torn off and sent into the fender while the front dragged on the ground. Resulted in broken knuckle, LCA, tie rod, and bent the steering, damaged the skid plate, broke the wiper fluid revivor, misaligned the passenger side fender and door, and damaged a rim.

(2): It drifted into a ditch at highway speed. Had to be pulled out. resulted in severely damaged rear tow hitch, damaged side plastic door trim, fuel cap, and a slightly bent rear frame. (barely noticeable and is only where the tow hitch attaches.)

I had known about the misaligned fender and unusable tow hitch for a while. It was only when I noticed bare metal showing on the fuel filler cap and the edge next to it where the two had been scraping against each other that I decided to take a look. I figured it's been sitting waiting for maintenance so I'll do some myself.

I've taken note of everywhere the body panels no longer align and various rust spots I need to fix. The front left fender, front passenger side door, front, rear left passenger door, fuel filler cap, and front bumper no longer align properly. It's a very minor thing but I'm wondering Is there anyway to move them back?
The frame is in good shape and not bent or severely damaged. (aside from the tow hitch i'm not even going to bother)
Any help is much appreciated.

So many of us here really enjoy our 4runners and take a lot of pride in them, but we all have different amounts of time to put into them

I know there are some videos on youtube of people gently using mallets to adjust body panels.

If it were me, I would probably try to spend a day removing the panels - IE the fender, the door, front bumper to see whats up. (its more intimidating than it is and isnt overly difficult or complicated.)

You can look and see if it is clips that have ripped/ need to be replaced or usually these pieces have small metal bars or brackets that they mount to

Just youtube "remove 4runner bumper cover" Remove 4runner door etc. If you cant find specific 4th gen, the 3rd and 5th are similar enough that it shouldnt be too dissimilar

to be honest.. some of the panels that can be adjusted, more than likely are not adjustable to the degree, or the direction that you need them adjusted.

For instance, the fenders and hood can be slightly tweaked to get an even fender-to-hood gap straight down and on both side... however, if your fender is contacting the door for instance, this is a tweaked fender apron that it sits on more than likely, or a tweaked fender itself.

Both of the accidents you described sound like they went a bit beyond minor. Without seeing some pictures of exactly what you're talking about it would be hard to tell... but for the most part, if you start getting into cases where you have some misalignment on doors (in particular the rear ones) that didn't take direct impact of some sort, it is evident of some degree of the frame being tweaked. I'm no body tech professional, but my brother does bodywork for a living and I've been exposed to at least some degree of various accidents and the sort of damage they cause.

If you want to throw up some pictures of the trouble areas you're talking about I think it would help point you in the right direction.

Ok there's a few things going on here. Most modern vehicles are built with tight tolerances so there's no shims or elongated bolt holes. If body panels are scraping each other something is bent somewhere weather it's a " messaged " body panel or part of the inner structure.if you see shims or elongated holes anywhere on a 4runner something is wrong.
Most likely you have a fender that has been messed with and it was deemed " that's good enough ".

You say fuel cap, do you mean fuel door? Those can bend from use. I've had 2 4runners that that has happened to both with new fuel doors. You can do small bending of the hinge to get them back right.

I would definitely get that frame rails checked. It can cause alot of issues if it's not right. It can cause suspension premature wear, rear steer, other body misalignment. Frame damage at a trailer hitch can transfer damage to other places on the frame as you have reinforced that area stronger than intended. Frames have crush zones on certain areas so that area has been strengthened due to the hitch so damage will transfer to other areas away from the hitch. Even though some 4runners came with factory hitches as an option, the frames remained the same.

Yes I mean the fuel door, if it's that easy I'll bend it back.
Otherwise the frame is still straight (again aside from the tow hitch). To clarify, the rust in combination with the degree of the bend makes it irreparable.
It did have some minor fixes to the front right of the frame after the wheel was taken off. Otherwise, it handles perfectly, and the tires have been wearing somewhat normal.
Only the fuel door is scraping the body. the passenger fender and door are close to doing so but just manage to miss each other.
I'll attach some images here

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1. Tow hitch bend
2. Fender/door
3. Passenger hood gap
4. Rear underside
5. Rear tow hitch
6. Rear tow hitch frame
7. Rear left door (upon further inspection it's the plastic trim)
And the front bumper has a few broken clips.

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The hitch bend is nothing, that's minor, still usable.

The fender gap does look tight, maybe an aftermarket fender. See if there's a black sticker with the VIN number on it attached to the fender jamb in the engine compartment near the fender weatherstripping, If not it's aftermarket.

Hood looks a little wider than normal, still could be the aftermarket fender thing.

Frame and underbody look ok except for that bump on the rail above the resonator. Not sure if that's just a chunk ready to fall off or a bigger problem underneath.

Flare looks like it just needs some clips or the clip mount has broken off from the flare. Easy fix. It's held on by orange and blue clips( 2 different sizes ). If the mount is broken off it will need to be reglued. A good urethane or plastic bumper repair work well. Get some of the clips, they will break when taking the flare off. When they do get a pair of pliers and twist the clip 1/4 the way as they are not the same size on 2 of the 4 sides. Also, when taking the flare off there is a flare "pad " on the top edges of the flare, don't loose it you need it. There are also 3 rivets that have to be drilled out. Amazon has the clips in an assortment, good quality.

Honestly thats a lot more minor that I was expecting. Mine looks worse that after off roading a few times. I think its probaby not worth the headache to try to stress about those things. Pick a few things that bother you most or gradually try to work through them. With body work, I always generally think am I just going to make this worse or can I improve it.

Id take a wire brush and scrape off the flaking rust best you can and then Id hit it either with rustoleum rust converter or fluid film black

good luck