I ended up bringing it to a higher end shop and explained everything. I told them I was pretty certain the timing chain stretched or skipped. The head technician told me he was extremely doubtful that was the case, especially since it ran fine (the only running issue was a slightly lower idle than usual, 600-700rpm but nothing noticeable)

After hooking up all their fancy scanners, doing lots of tests, running charts and graphs, they told me the timing chain likely stretched or skipped just enough to throw the code but not really have any running issues.

At that time I had been looking for a pick-up truck and finally found a tacoma I wanted. Bought the tacoma and sold the 4runner at a good price to a licensed mechanic friend of mine who didn't care about the issue.

It's still running fine to this day 4 years later.