If this is working out, then that's great! If it isn't, send me the unaltered captures of the laserdisc audio directly and I'll see what I can do with it. I would synch it directly to the '93 mix, since I don't have anything to run it with the video at the same time (and that's less precise anyway as Satanika said).

I think using small segments of the '93 mix to replace any gaps in the theatrical track would be ideal, then you wouldn't have to worry about stretching and pitch-shifting and all that rubbish. Short crossfades will ensure the absence of any jump-cuts between the different sources, but the exact transition points must be chosen carefully--be wary of transitions that may take place during a music cue especially, because then any differences in imaging and sound quality will be the most noticeable and distracting.