The first rule in debugging is to strip the system down to its minimal configuration and then if there's no problem, add items in one at a time (note that you might be able to debug both the ground loop and the popping at the same time using this method).
First, unplug everything from the amp except the speakers. Turn the amp on and see if you have any pops. If no pops, plug in the preamp, connect it tot he amp, and turn it on. Listen for a while -- any pops? If no pops, plug in one source. No pop, plug in another source, etc. If the first source has pops, then you haven't necessarily ruled out the preamp or amp. Unplug the first source from the preamp and plug in a second source. If you have pops, then it's not the source, it's the preamp or amp. To test the amp, if you have a source with its own preamp (some CD players, Squeezebox, etc.), plug this directly into the amp and play. If you get pops, you haven't ruled out that source, so use that source on a different amp and speakers. If no pops, the amp might be bad.
I hope this makes sense.