I was luckily enough where the nut seized onto the stud but was able to back out the stud.

I was unable to extract the broken stud, but was able to cut / grind down the broken stud with a Dremel, then drill through with an 1/8” and 1/4” drill with 12” extension, and then use a through bolt and nut.

Do you have a link for the extension you bought? I have the same issue on my 2018 4 Runner (both studs!). I have the studs ground flush, but I am struggling to find something to get a drill bit to reach the flange area.

Edit: So I got it sorted and just in case anyone stumbles across this thread here is what what I did...
- First, the only thing I could seem to find outside of the McMaster-Carr rod-with-a-collet (expensive) was a "drill chuck with a 1/4" hex shank". I couldn't find it locally so I ordered from Amazon and it was delivered by 10:00AM the day after I ordered it.

By 10:15AM I realized why it cost $9...the entire thing disintegrated halfway through the first hole. Fortunately, I remembered a local hardware store that somehow seems to have everything so I gave them a call and sure enough, they actually had one. It was made of steel and it did the job, though I'm not sure it will last a lifetime...

After that it was a matter of getting the drill centered and taking my time not to break anything. I ended up using the magnetic bit holder extension that I happened to have available, and that was pretty wobbly, though it did work. But if I had it to do all over again, I would order an extension that had two set screws to lock the drill chuck hex in-place (search for "Spade Bit Extention" to see what I mean).

Also, I drilled it to 1/4", which is slightly larger than the 6mm stud. And I did it in one shot, rather than start small and progressively drill it larger. I reason that it's a lot harder to break a 1/4" drill than a 1/8" drill, and I didn't want to have to deal with getting a small, broken drill out.

BTW, I didn't get an estimate of the cost to bring it to a dealer, but if I were to guess, I'm thinking it would be the better part of $1K if the manifold had to be replaced.

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