I think Eric was just loaned the Jaguar. Apparently famous musicians do that to bands they like. In my travels for jazzy pics I found out Ric Ocasek loaned his pink Jazzy to a band called Rooney that he produced, and STP loaned a few guitars for Sonic Youth for gigs during the early 90's according to their guitar database.
I also read somewhere that the Jaguar was the guitar left in trust to Francis, not the Mustang, it think it was on OSG where I read this.
I think I've seen Kurt's Competition Mustang at the Experience Project in Seattle about 2 years ago. It had the vibrato bar on it, but still had the TOM and the vibrato looks to have been locked, and I recall seeing some cracks from the neck damage at the Texas Trees gig where Kurt smashed it into the soundboard. They also had Krist's Ibanez bass too (which looked like hell BTW).
The Jag-Stang I'm sure is still with REM. I have never seen them use it live though. I heard it is used for "Let Me In" but I Can't find any footage of the guitar in use on that song. Actually, the only place I've ever seen it is the "What's the Frequency Kennith" video that everybody knows about.