This sounds like a logic board issue to be honest. We have repaired thousands of headphone jacks and personally I have repaired a few hundred of these. There are many cases where the audio channels on the logic board have issues causing the "underwater" sounds you are experiencing. I have also seen the logic board be the cause of the single side headphone jack failure. In fact the headphone jacks are usually 100% working in these cases but the logic board is where the problem resides. It is also sometimes tricky testing this through the dock connector but by checking audio through the dock connector you may be able to determine if it is actually indeed a board issue.
If you guys need help with boards or headphone jacks or any other type of iPod related repair give us a shout.
