I haven't ever payed too much attention to mega-changers, and they've generally not been considered the domain of really top-notch players. Since you can simply pipe the digital output to your Yamaha (or the 990 you were considering, if you make that move down the road), you really just need a decent transport, though, so I'd expect that any of the Sony or Pioneer mega-changers would be safe choices. Probably the biggest question there is how good the user interface is when it comes to trying to find a specific disc in the changer. Some of the mega-changers allow you to plug in a computer keyboard to help enter artists and disc titles more easily, which would help with the disc management. The Sony and Pioneer Elite changers both include keyboard support.
iTunes does not support copying files from an iPod to a computer, but I did find a couple links indicating that it can be done.
This article seemed like a particularly good resource.