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I'm looking for a material that could be used as a temporary repair until the mechanic can come out and do the repair properly.
Vic,
Since I posted earlier today, I've been thinking more about this (while I was cleaning my cockpit!).

Ken's right that pictures would help us to help you. He also describes the studs on the gear cover quite well.
But before you jump to the conclusion that you
need a new gear cover, please know that they are almost impossible to find, because so many M25 engines (not M25XPs that came with the new alternator bracket) had their gear case covers clobbered by failing alternator brackets on the M25 engines, that they literally ran out of gear case covers.
I wrote to a number of friends about my issue early last year, including Ken. Ken said pretty much the same to thing me that he did for you here. Others had other suggestions.
I have, so far, chosen to NOT go immediately to the replacement cover. Why? 'Cuz I don't think I can personally physically do it, having carefully investigated the work involved. I'm sure, for example, that I would be able to get 11 of the 12 bolts out but that last one won't want to come out and I'm not enough of a mechanic to figure out how to do it when, not if, that happens. And my bolts, all of them, have been there for 32 years. Some of them I'd painted over years and years ago, which doesn't bode well for any sort of easy removal. The closest mechanic to me who I know and trust is a three hour motor to get to his yard, and my engine still works. They don't do house calls here.

Wouldn't make sense for me to do it in my own slip and get hung up there, would it?
I'm sure I could deal with most of the ancillary issues like dropping the alternator (that I could do in my sleep), but the engine stop lever part on the starboard side gives me great pause. I simply don't want to mess with that, having researched the brain salad surgery required for the little spring inside that housing.
So I opted, after careful reflection, to attempt to rebuild the failed part of the gear case cover casting (it's aluminum).
Where I am now is in the "testing period" of my third repair done in November, the JBWeld worked to build it up, but wasn't strong enough to hold the new stud in what I call the September second try, so this third repair is the first time using the Devcon as the glue.
The first repair attempt in March was stupidity on my part by not recognizing the extent of the decomposition of the casting shown in my first picture. I just took the pump off and rebuilt the seals, not looking closely enough at the pictures I myself had taken in March. In September's second repair attempt I tried JBWeld as the glue and it failed in 20 hours, never having held the new stud in firmly.
I've now got about 22 hours on the latest Devcon November third repair and am keeping an eagle eye on the situation. I plan on local cruises in the near future to use the engine, see what happens and not be far from home if it doesn't hold. It leaks a little oil when it fails, but a little oil makes a BIG f-ing mess.
Are you sure your pump seals are working? Any evidence of water seepage out the weep holes that could have zapped your stud and nut?
As for the ? in what I quoted above: No, I can't think of any "material" that you could use for any temporary repair if the threads on the stud are gone.
If your engine still works and "all" you've got is a rusted nut on a failing stud, using the engine should be fine but with my experience in hand now, just be aware that you may see an oil leak if the failure allows the pump to loosen up on that one quarter of its four stud support.
You didn't say which stud & nut failed. Was it one of the lower two?
And before you "trust" your mechanic, you should talk to him in
great detail about what he plans to do
before you have him even touch your engine. Let us know what he suggests.
In my case, I experienced an oil leak, so the very first thing I did was remove the pump, mistakenly thinking it was the pump oil seal. It wasn't, but I'd had 800 hours since the last seal replacement and the one before that lasted 1300 hours. I was thinking pump seals when I should have been looking at the decomposition as I described above.
What I think happened was that the fourth stud's gear case cover metal disappearance allowed just enough space to grow between the gear case flange and the pump base to let the oil inside drip down. That pump
needs the four bolts to keep all of the faces together.
Also, just for the record, and in anticipation of respondents suggesting that water through the weep hole could have been a cause in my problem, I did NOT have water seeping out of the pump weep hole, so the failure on my engine wasn't from neglect of the pump dripping water on the stud and nut. The nut that was there was just fine, but the metal holding the stud in underneath the pump base and in the engine case cover flange simply just disappeared!
It was an interesting way of getting a stud out of a Kubota engine. All done without a propane torch!

I'll be interested in any and all other observations about this, and certainly from you about what you learn about your situation.
I wish you the best of luck. What I've found in this and other boating situations is don't rush into anything. Analyze, think, talk to trusted friends, trust your mechanic only after you talk to him and check his credentials carefully unless you know and trust him already.
It just occurred to me that I don't know if there is any forum like this for Universal M25 Series engines. Gee, wouldn't that be helpful?

Please keep us posted.