All of these things, I'll grab the

opcorn:
I really want a rack, but this got me scared as he!! now. Did you see any damage to the inside headliner at all that would indicate any issues? I would assume with that much damage that you should have started see water issues in the headliner or at the inside starting to smell all the time.
Also, is there a reason that you removed the rack multiple times in the past? I had a rack on my last 4runner for over 6 years (parked outside) and never once thought about removing the rack once it was already up there.
Whats done is done.If you trade it in or sell it (be upfront). you probably wont get much for it.Take it to a body shop that deals with classic restoration and ask them to evaluate it and see what it costs. If you can afford it get it fixed and make it your forever vehicle or cut your losses and move on. In either case it's going to be costly.
In the pictures it appears the inside of the roof is scraped away as if a grinder was used on it. The bolts and brackets also appear to be a mis-matched set. Did you have to drill new holes and such for the full length rack? If so, did you repaint the cut metal to protect it or just seal with permatex?
Wow! Just wondering, did you park your vehicle in a garage or out doors all if its life? I’m wondering if I should seal my roof rack mounts. I do park in garage when at home and live in sunny California.
Wow, that’s hard to imagine. Did u have any water leaking and puddling inside any where or staining onto the headliner? Need to check my rack on my LX.
I am going to try and answer some of the questions and responses to the thread.
I bought the truck brand new in 2014 and half of its life garage kept in San Diego. The next half was in Hawaii not garage kept, the issue both places is I was frequently gone often so the vehicle sat static for periods of 6-7 months.
The roof was line-X in 2016 when I got to HI as well as the rack (1 of the times I took the rack off, I can't remember why I removed it the 2nd time). I never saw any indications of the roof leaking and never had water coming in. I deployed several times from HI and the vehicle was left outside for long periods of time. I assume had there been water leaking, it would have been apparent when I returned with either mold, foul smells or some sort of sign, but there were none. The photos posted are of the top of one mount with one bolt in and one out and the inside of the same mount, as well as the headliner(excuse how dirty). My intent in the photos is to show it did not really show signs or indications, not like you would expect with the amount of rust
The original photos I took were after I did some scrubbing of the area and some of the bolts were different due to the sale of the rack I also gave up the original hardware, so I put something to place hold until I can get more factory bolts.
For those concerned about an aftermarket rack I assure you this was pretty much self-induced. Had I sealed properly and regularly checked the seals this probably wouldn't have happened, also the factor the truck sat static for periods of time allowing water to soak in didn't help.
I don't really plan on selling it, I'm going to figure something out. I will probably hit a pick-in-pull or something to try and pull the sections I need. I have no idea or experience how to weld but I do have youtube. I love this truck and very much love not having a car payment. The truck is also in great mechanical shape I barely broke 60,000 miles a couple of days ago. Hopefully, this just serves as a reminder to CHECK YOUR SEALS!!
On the upside, I'm stoked this post has over 2,000 views and a ton of comments ..lol