That sounds like a good price for a rebuild at a dealer but I'm not surprised by which dealer that is, Bob's. Look's like the bare minimum parts tho, nothing wrong with that, probably all it needed. Bob's is one of the few dealers recommended regularly for Airhead repair and that includes transmissions.
There are maybe a dozen known mechanics around the country for Airhead 5 speed repair. It's recommended to use somebody with experience and a proven tract record. This does mean that sometimes you will have to ship the trans to somebody who can do the work.
In the bike the best indicator of problems is metal in the oil, on the magnetic plug, when the oil is changed. There will be a bit of soft black substance on the magnetic plug of a healthy transmission. This is soft when squished in the fingers. The danger signal is gritty, starts small like sand grains, particles. This harder metallic swarf is disintegrating bearing metal. If you find hard gritty metal on the magnetic plug the trans is ready for a rebuild. It can be postponed for a couple hundred or a couple thousand miles but it gets worse and the longer you wait the more expensive it is likely to get.
High mileage 5 speeds get several problems that indicate repair needed. False neutrals, whinning bearings, missed shifts. Some of these are expensive to fix and some of them you can learn to live with.
That's all for now. You don't mention what year 5 speed. Like most other parts on the Airheads the transmissions went thru a lot of changes. Repair options will depend on the vintage.