Cleaning albums is a big topic over at AudioKarma but I keep it pretty simple. A little Dawn detergent in a spray bottle of distilled water and then a soft paint brush run along with the grooves a bunch of times and then rinsed with more distilled water. Dry them with a micro fiber towel and then let them sit in a dish rack for a bit before playing or storing them. I protect the labels with a contraption made of wing nut bolts and gasketed round electrical box covers. Works well and makes a pretty big difference in the playback.

Since I'm storing the files in AIFF I'm not sure if I'm going to keep the .aup files because I can edit an AIFF in Audacity too. I can also use iTunes to make mp3 or AAC versions for my iPod. Its not the original "recording" but probably close enough. Though I can see how keeping the .aup file would be handy. Mmmmmmm, I may need more hard disc space!

So you are not using the phono preamp of the Behringer, just the ADC? I'll eventually have that configuration which should be better as I'd expect the phono preamp in a '70s Pioneer to be an improvement over the preamp in the GemSound.

Are you breaking up the recording into songs or are you leaving them as one big file? I'm trying to figure out the best way to reduce the surface noise between tracks but not make it so quiet that it sounds funny. Any suggestions?