Finally success!
I found this post in a forum which gave a hint as to what the potentiometers actually control:
http://nfggames.com/forum2/index.php?topic=2890.0 I'll paste it here also:
POT = Function, Test PointVR101 = E/F balance, pin 13 of U101
VR102 = Focus Offset, pin 18 of U101
VR103 = Track Gain(Track error level), pin 45 of U102
VR104 = Focus Gain, pin 48 of U102
VR105 = VCO, pin 30 of U102
Not sure exactly what all these mean to be honest, but it was enough to help me decide which pots to adjust and which to leave be.
I adjusted VR103 slightly until I got consistently good skip-free playback. I think VR103 controls how sensitive the laser is to end of track markers, and my system was previously too sensitive.
Now all I need to do is get some descent cd-rom games!