The biggest problem that I have with this method (other than head gaskets) is that without removing the heads, you can't get a tool down into the bolt holes to clean all of the accumulated crud out of them. If you can't clean out the holes, then if there is any crud in them, and there usually is, then the stud won't be able to go all the way down into the hole. This will leave the stud sticking up higher than it should and can cause clearance issues with your rocker arms. Besides, after 30+ years of abuse on the old ones, new head gaskets are always a good idea. Even without a turbo.
Plan was to use a spiral bottoming tap, with a tap extension, and vacuuming/blowing the hole out with compressed air after. The extension OD measures a hair over 7/16, so I felt I wouldn't have fitment issues doing that. I've got all that in the shop already, so the cost is nothing.
Yes, you're supposed to use a thread chaser vs a tap, but with that long of an extension, I don't think I'd have issues going in straight and cross threading the hole. The spiral flute would help to pull the crud out as well. The little bit of metal removed using a cutting tap isn't a concern for me either. I doubt the strength of the threaded bore would be compromised if it was missing a thou or two.
I've done bolt to stud swap on 6.0's and gas LS engines with stock gaskets. Granted, those all use a MLS gasket design, but the stock idi gasket isn't a sponge material, so the gasket compression difference between a bolt vs stud can't be that much.
My thoughts, is if I'm going to pull the head to do gaskets, I'm having the heads machined flat. There's no sense in throwing gaskets at a bad surface, and I've never pulled a head and it be perfectly flat. Then, if I'm pulling the heads to surface them, I might as well put guides and seats in them, because those are likely worn too. And then I might as well machine the block too at that point, so I know both surfaces are good and the gasket won't have issues. If I'm pulling the block to machine it, I might as well rebuild the thing with new rings and a fresh bote, because there's no sense in not doing that at that point. So a head gasket job pretty much ends up being a total rebuild for me, and rebuilding an engine that gets ran a few hundred miles a year is foolish in my eyes.
Just a note, my idi is in a bus. So I can do the bolt to stud swap without any cab interference. I don't think you pickup guys can do that. I believe pulling the heads is a must to install studs in a pickup.
Stud install on the 6.9 will probably be dependent if I can get a set of them for cheap between now and the turbo install. If the gaskets blow on the 6.9, then the spare 7.3 will likely be swapped before I rebuild the 6.9.
