Here are the options that I've considered, but wonder what others of you think:
1) Just put both mixes in together. This does very little to fix the swapped music problem so it's a crappy option to me.
2) Simply plug '97 rear where 2004 rear is. Not a great option because a lot more mixing is present in the 2004 version.
3) Run 2004 rear in dual mono (send both channels to both rear speakers). You lose the panning effect of the rear, but you still have an effective rear separate from center, right and left.
4) Run regular rear-stereo 2004 simultaneously with a copy of the same tracks, but with lowered volume and dual mono. This will normalize the music somewhat, but not all the way. Some of the instrumentation will balance out, but it will still be stronger in the wrong place. However, this will help preserve the FX somewhat as well. May be the best compromise.
5) The pain-in-the-ass method I was trying for a while where music-only cues were flip-flopped (to correct them), but cues with FX present were run as they were presented. Too damn much work for a half-baked solution.
I have mixed the old Krayt sound with a smidgeon of the new, restored the 1997 echoes in the chasm, the fanfare, and restored the "he's on your tail" line before Red 5 bites it.