Eric,
I am assuming based on the boat you have listed in your profile your radio is a Sony MEX-1GP. If this is the case my suggestions are as follows.
For #1 try inspecting the larger of the cables that go to the remotes at the stereo or Y connector. This is the cable that supplies the display. If you find it disconnected or not making a good connection, obviously reconnect. You will have to cycle power on the head unit for it to redisplay. (Just verified on mine). If this does not work try connecting only 1 remote at a time.
For #2: With the head unit off, but still having power to display the clock, press and hold the select button (Volume). It will first display clock adjust. Press the select button to cycle through options. When you get to the AUX turn the volume to change it to on if it is not already. I found if it is off it will not be an option when you cycle through sources.
For #3. I am not sure.
. Does it still pop if you change tracks with the head unit instead of the remotes? My guess is if you get your IPod going the popping will go away. Temp solution
Again this is only for the MEX-1GP though it probably is fairly universal for Sony. Let me know how it goes.