The rubber PH perimeter seal and rubber caps should be readily available on the SMB site. A few notes.....the seal isn't pre-punched for holes, although it does include the plastic fasteners......I used a single paper hole punch to poke the holes.
Also the plastic caps are cheap but do not include the metal washer under the cap, for some reason SMB is really stingy handing these out. There is a recent thread about where to get those.
I would also consider replacing the cheap hardware (bolts, etc) with stainless. Stainless fasteners are cheap and easy to obtain. Several of us here have used stainless self sealing washers on the roof, they are available from McMaster carr. Search for a my thread called "popping my top" or Bmerritt's thread, we used different washers but you'll get the idea.
The blobs of butyl rubber under the roof washers can be renewed with Butyl tape available from McMaster if you are so inclined.
2008 E350 RB passenger 4WD SMB penthouse
2013 KTM 350 EXC
2008 KTM 250 XCF-W
2000 KTM 200 EXC
2003 Honda Element