Hi Chris,
The issue regarding the 'blown earth track' usually yields a continuous background noise through amp driven speakers, this noise is not relative to engine running/speed in the same manner as a 'ground loop' induced alt whine....
The 'popping' issue you mention is related in most cases to a poor earth, (when using ext amplification), or an internal head unit/amp fault....I would suggest you try earthing the head unit chassis and the head units iso loom earth direct to the same point on the cars chassis....(the stock audio looms earth usually earths at the same point as other circuits and so can suffer higher than usual resistance).....
It's not uncommon for head units to drop a channel if a speaker terminal shorts to ground, (Amplifiers carry +ve voltage and -ve voltage supplied via a switching power supply which essentially means both speaker wires carry power, +ve voltage pushes the speaker cone outward, -ve voltage pulls the speaker cone inward), reversing a speakers polarity simply changes it's phasing, it will not cause the loss of sound you suffered.
It sounds like you could have a faulty speaker, or possibly a faulty head unit, without actually checking it for myself I'm only guessing. If you now have full range sound from all four corners I would try earthing the unit as above....if no joy, let me know....
Regards...john..