Leaks from the shaved roof rack

[killthewabbit]

So, just got my 99 Tahoe 2door 2wd a couple weeks ago. Someone before me removed the roof rack, but the holes remain. Two have the cut off bolts in them, but 6 holes still have holes that water could get through. It rained once last week and I noticed a big drip inside. Today I tried to seal that one up and clean/reseal the other holes with black gasket maker. Since this is a thread now, you can guess my results.

Point of all this is, what did everyone who shaved their rack use to seal up the holes? Any ideas? Obviously I'd love to get them welded up and painted, but what should I use in the meantime? I'm gonna vote against black gasket maker.