Flyview: Consider removing the nuts and washers on the roof and re-applying fresh butyl rubber sealant. McMaster-Carr sells butyl tape, it's what SMB uses. It' unvulcanized (uncured) rubber so you can rip off pieces to put under the washers and clean up the excess once applied.
Also consider sealing washers if you are ordering from McMaster..they are stainless and have integral washers.
The plastic caps that go over the roof nuts are available from SMB for cheap, but are just cosmetic.
Here are some stainless sealing washers from McMaster:
I'd go for the 18-8 stainless 1/4" x 1" OD $6.78 for a pack of 10
...and here's the link for the tape...
To clarify, I used the sealing washers on top of the large fender washers on the roof...If you are so inclined, stainless 1/4-20 fasteners and fender washers are also available from McMaster.