So I have tried searching this, but can only seem to find MANIFOLD bolt related threads, I am having an issue with the bolt (or stud) which connects the manifold to the exhaust flange.

It is on a 22RE, there are 3 bolts/studs which pass through a flange on the exhaust. The bottom (or front??) 2 are on, but the one at the top/back of the flange is missing. The previous owner said it got stripped when he was doing some work on the exhaust last summer.

The result is that I now have a gap around the top edge of the flange which sounds like ass, and results in some backfiring and an intermittent check engine light (which I assume is feedback from a sensor on the exhaust).

The threads don't look super trashed, might just be the starting thread. I went to the Toyota dealer and bought an expensive nut, which is supposed to be the right one. But I can't get the nut started on it, and there is not really any room to slip a die over it & spin. Have also tried the cheap and cheerful fix of exhaust stop leak, which works great until I drive over a bump, when it craks and falls off.

Any thoughts or tips on how to get this sorted?

 

You need to drill it off or use heat and a good bolt off socket and get it off, then use a nut and bolt in place of it.

 

Aside from pulling the manifold, take the nut you purchased from the dealer and file the inside threads straight across to make a die. If the nut is hard and can not be filed, have it heated cherry red with a torch and let it air cool to anneal it soft. Next stop, your local ACE type hardware store and get a small quality V shaped file. Go home and file 3-4 groves across the nut all the way to the base of the threads. You now have a psuedo tap. Back home, take a flat file and put as much of a point as you can on the buggered stud to make chasing the threads easy to start. You will have to put a lot of pressure on the nut and slowly rock it back and forth, in very small increments, to get it started. USE ANTISEIZE compound when doing this feat. Eventually you will prevail. Once the nut hits the manifold, remove it and replace it with same nut from another manifold stud to ensure you got the right one. Careful not to strip that one. Then go back to dealer and get another nut. Option #2 is to pull manifold and heat the stud to remove it with a stud extractor tool.

My $0.02

 

Good post.

The nuts are much easier reached from under the truck with a foot long extension and a deep well 14mm socket from Lordco.