Im getting ready to install my prinsu rack and of course it won’t be an 80 experience if everything went smoothly

. 2 out of 8 welded nut came off. I plan on using SS bolt with rubber gasket + toyota fipg to seal the holes but not sure what will be the best with the other 2 holes without thread. Welding and painting is not an option at the moment but definitely in the future if I need to replace my windshield or something. I live is southern California and the truck is garaged so it will not see a lot of rain.
Should I just use some plastic plug with fipg to seal the holes? I heard jb weld will crack eventually. At least fipg sealant is pliable with stress?
Also do I need to remove the 4 horizontal bars on the roof prior to prinsu rack install?