Hi. I'm really sorry to hear that. It's definitely the clutch splines. You need to make some seriously hard decisions about that bike. In a functional state it's worth about $3000. Fixing your problem will cost from $1000 to $2500 depending on how you go about it. It may not be worth it to fix.
In my opinion your best bet is to replace your transmission with a known-good used transmission. Between that and some new clutch parts you might be able to get away with spending a grand or so. There are several on eBay right now. You need to make sure you don't buy another bad one. The one in the first link below is bad. In the second pic you can see the wear on the input splines. Don't buy it. the one in the second link may be OK, but don't buy it until you get a few good pics of the input splines to make sure they're OK.
A quick note, nrpeterson is mistaken. As you know, the R1100S has the six-speed transmission, like the 1150 series. The five-speed tranny that goes in the rest of the 1100 series is in fact a different animal. Speaking of that, it would be interesting to know if a transmission from one of the other bikes in the 1150 series would fit. I'd be a little surprised if they did. I've never studied them side-by-side, but I think the mounting points are different. Mike at Beemerboneyard will know.
1999 BMW R1100S OEM Transmission | eBay
BMW 1999 R1100S 6 SPEED TRANSMISSION - LOW MILES | eBay