We're nearly there, folks . . . I listened to the test file today and I need to go back and lower the LFE level a bit in a few places--I had overcompensated for the oddly subdued volume sometimes found in the SE's. The newer versions tend to let their loudest bass impacts come from changed CGI shots or added sound effects; I toned those down considerably and gave the original bass moments greater prominence, but inadvertently overdid it in a couple places. I haven't been able to turn it up as much as I'd like for fear of disturbing others, so I'll have to check again when I have the place to myself, but even at low volume I could tell I hadn't done it right. Fortunately, these should be easy enough to fix.
You're right about the 1999 Alien dvd having an isolated score track--but I only have the 2003 version, plus the cd is said to sound better. ;)