Thanks for the replies everyone. Here's what I did: Well actually here's what I had done. Mike I took your advice and went to Fletcher's. I nursed the bike along the higways in third gear, scary! But when I got there Mr. Fletcher felt the shifter and figured out that it was a shifting problem and not a transmission problem. He said that he could machine the parts if needed, by which I think he meant shift forks.
When he finished he called and told me that the bolt holding some part of the shift drum had loosened and come off and that it was a good thing we stopped riding. So Scott I think you were right about the linkage, but I didn't realized you could get to all that from behind the clutch.
The other problem is that I contracted food poisoning while in Memphis and so I haven't been in a position to work on it myself.
The repair wasn't cheap but Fletcher knew what he was doing and got it done quickly for us. Great shop for anyone who doesn't know!
Thanks again, we're back on the road. After (finally) visiting Sun Studios we're off to the Ozarks!