Ok, so I finally found the time and collected all the parts required to repair the front roof rail for my brother's '94 YJ. After many good suggestions, I decided to go for the installation of rivnuts in place of the factory screws, plus drilling a bunch of new holes for rivnuts in an attempt to compensate for the cracks in the old holes. This seemed the fastest and most economical option, since time was a factor in it as well.
To start out, I went down to Harbor Freight to pick up a rivnut kit figuring that even if the rivnuts themselves weren't suitable I'd at least need the installer either way. As a test I selected a 10-24 rivnut, drilled a hole in a scrap piece of 18 gauge steel sheet, inserted the rivnut, squeezed down on the handle of the tool... and promptly ripped the threads clean out of the rivnut. And that wasn't with much force applied, either, which said to me that Harbor Freight's rivnut offerings simply would not suffice for this repair. Not surprising, I know, but it was worth a try.
So, I figured I'd go with the more rugged option, and headed down to Aircraft Spruce to pick up some REAL Rivnuts, as in the name brand version. Additionally I purchased a bunch of aircraft grade bolts and washers to thread into them since I didn't want to skimp on anything. Keeping in line with my normal bad luck, Aircraft Spruce doesn't carry
10-24 rivnuts... I had to buy 10-32, which meant my tool from Harbor Freight was also now useless. Tack on another $28 for a 10-32 rivnut installation tool from Aircraft Spruce... ouch. But, these rivnuts can definitely take a load better than the Harbor Freight ones. You can really crank down on these and not have them strip.
With all that out of the way, I mounted the rail onto the window frame using just the two outside edge screws, redrilled all the holes so they were big enough to take the new 10-32 bolts, and then removed the rail and drilled the window frame holes large enough to accept the rivnuts. Next I installed the first series of rivnets. With that done, I reinstalled the rail and drilled even more holes, plus drilled out the two outer edge holes I skipped in the first round. In order to compensate for the additional metal added to the window frame by the rivnuts, I lightly tapped the installed rivnuts with a hammer to sink them down just enough to make everything flush. In cases where the frame was cracked and wouldn't properly handle this, I created a divot in the rail that would clear the collar on the rivnut using a hammer and an open vise as a backing against the rail. Worked pretty well overall, though it did take some slight tuning to get everything properly flush once it was entirely installed. No big deal though.
The end result looks like this if anyone wants to see:
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There's not much to see, really, but I must admit I do like seeing those cadmium plated aircraft bolts holding the rail down. It certainly looks like it's not coming off any time soon, but it can still be removed if necessary.
Thanks again to everyone for their suggestions, it looks like this is a repair that should even be able to survive my brother's mechanical curse!