Ted, when you use Vegas to do the stretch, do the two files typically line up throughout or is there any mid-file mismatch? If there's a mismatch, how is it to correct the mid-file drift using Vegas? (I'm not a Vegas user, but I'd think it might get a bit hairy if there's not consistent straight line drift between the two sources.)
FWIW, I've had experiences both ways, where I'll stretch a file and it synchs well with the file I'm trying to match, but then I've had some where they don't line up great in the middle, even if they do line up at the beginning and the end.
In either case, when they don't match up, you need to line the tracks up so they're synched at time = 0 and then choose one or the other of the tracks to 'massage' all the way to the end of the set to get them paralleled with each other.
For those of us that don't have Vegas, you can do this in the multi-track view of your DAW one of two ways that I know of. You can try to stretch/shink small portions of the second track as you progress along the timeline of the show so that it matches the first track from t = 0. Personally, I find this method to be a complete PITA and it never works right for me anyway.
My preference is simply to delete tiny portions of the second file a tiny portion at a time along the track, starting at t = 0. You can do this a song at a time or you can do a complete set at a time, as long as you build each master file starting from t = 0 with both files synched and keep them matched started from t = 0. As long as you zoom way in and you only delete tiny portions on the second track, you can't hear the deletes...especially on a mixdown. It's easy to keep the tracks lined up like this. (hint: save often!)
I don't find it to be particularly difficult or really all that time consuming to synch two tracks when I use the second method (a couple hours for a show). The key is, when you're lining up the tracks, to zoom in enough so you're focusing on individual notes along the timeline of the performance and make sure the two tracks are never more than a millsecond or so apart from each other, otherwise you'll hear the time delay between the two tracks as being overly reverb-y or echo-y on your mixdown master.