From my perspective you have two ways to go either your going to repair it or sell it. I had a 1998 that had almost the same history as your 4runner. I repaired it but decided that I wanted something a little nicer after I was done i put it up for sale. I did not pull a CarFax but the wear did not reflect the mileage on the 4Runner. When i sold it I was up front to buyers telling them that i did not think the Odometer was accurate and let them decide what they wanted to do. The guy who purchased it seemed ok with it and have not heard anything either way after the sale.
If you like the 4runner compare it to replacing it with something you would like to drive. I am Not sure if you are going to do the work or have it done if you did sell it I'm sure there is someone who will enjoy this as a fixer upper. I would just hate to see something like a Ball joiint failure or P/M issue causing something bad to happen.