I have a gut feeling that this problem is due to simple component drift, and
not to the need for a complete alignment.

Am I correct in assuming that resetting the VCO control restores stereo
reception? If so...

Try replacing the pot with a cermet trimmer. It should have better long-term
stability.

When I owned the Heath "Most-Accurate Clock", I had stability problems that
went away when I replaced the carbon calibration pots with cermet.

Just a thought.