Gear box blues

My two year old 95 1100Gs is down and out. The dealer informed me, that the noise I beleived was from the final drive, but rather, it is the gear box. Plus the final drive may be damaged. The bike has 34K, 12k by me in the past two seasons. Should I seek a second opinion? For now, the repair will have to wait, especially since I was quoted $4-5K. I have a lot of new items invested, but that quote is almost what I paid for it two years ago. Or, should I part out the bike individually, or as a rolling chassis? Clean title.

I would look for a good used transmission. I saw one on e-bay a while back. they can be had for less than $ 1,000.00 good luck...

Here's everything you ever wanted to know about R1100 transmissions: Anton's transmission page.

I had the transmission in my R1100RS rebuilt about two years ago by Tom Cutter. 40k miles later, it shifts even better than when I first got it back. A rebuild will cost somewhere between $1k and $2k, depending on exactly what's wrong. (That assumes you take the trans out of the bike yourself - it's a pain but highly doable.) I'd feel more comfortable about a pro, like Anton or Tom, rebuilding the trans instead of potentially buying someone else's problems with a used one.