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Heya, came across an oem roof rack from a '90 240 at a pick and pull and found a website that sells all sizes of threaded grommets. I know the thread size of my well nuts are 1/4" but you should do all your own measurements to make sure they're identical. Nothing worse than a leaky roof.
At least, don't buy them if it is ever going to rain on your wagon. I bought a set in 2008, after I foolishly removed my roof rack to deep-clean my roof. I was unable to reinstall the rack because my gaskets shrunk, so this seemed like a decent alternative. Unbeknownst to me, rainwater seeped in, collecting on the floor deep under the carpet and rubber mats. Years went by, and I was left with a rusted out floor that needed to be replaced at great expense. IPD is located in Portland, where it rains as much as it does here in Seattle. They should know better.
I have used 3 sets of these IPD plugs (I remove and junk those racks ASAP), and never had any issue with leaks...
The metal around the hole you plug up has to be perfectly flat and even. When removing the rack grommets sometimes the holes get distorted, I think I see that in the picture, then the plugs cannot seat well which will cause leaks. Once the metal is distorted, it's hard to flatten it again easily so I guess caution should be used when popping up the old grommets. One is limited as to ways to do that, a screwdriver prying them up seems like the most sensible option but that sometimes causes the distortion.