Those "rubber nuts" is called "well nuts" - they're a rubber surround around a brass threaded insert. The screw is threaded into the insert, then the rubber gets pulled up to surround the plate and fill the hole as the screw is tightened. It doesn't take a whole lot of torque.
IIRC, using #10-24 or #8-32 well nuts will fit neatly into a 1/4" hole - and the holes in the roof should be 1/4". Therefore, buy whatever size well nuts at the local that fit in a 1/4" hole (about fifty cents each) and flat head machine screws to fit (about an inch long) in brass or CRES.
My rackmounts were leaking, I peeled the rack off and got brass pan head screws and well nuts to fill in all of the holes for about six bucks all up. I'll eventually have the holes plug-welded once I get a patch panel cut out to remove the damned sunroof...
