My Cannondale has disc mounts, but came with rim brakes, so we decided to add a rear disc brake this year. I bought a set of Avid mechanicals and a disc rotor adapter that threads on the non-drive side of the rear hub. The brake and rotor don't come close to lining up. Are there different thickness rotor adapters available? Shims? Has anyone tried this? I contacted Cannondale, but they were of no help.

Yes, there are diffent sized rotor adapters. Call Tandems East or Precision Tandems to get the right size adapters. There are also shims avalable that go behind the disk or for the caliper mount, but they are usually for small adjustments.

I had the same problem when I put a disc on the rear of my Cannondale. I'd recommend tracking down the correct size rotor adapter. I used shims behind the adapter but it just wasn't the best way to go. I ended up getting a disc specific hub for the rear and kept the V-brake on the front.