Suggestions? <snip> Am I just not seeing the obvious here?
IMO, the obvious solution (and not the answer you want to hear): spend $50 on Samplitude SE v8.
Using SSE's Virtual Project mode, you keep all your individual files (don't need to join them since you join them virtually in the project), work on or edit all files / objects within the project jointly or independently, split files into smaller objects and apply different effects to different objects, add tracking and fades within SSE so they're easy to regenerate later (no need to dump out to WAV, then open CD-Wave and apply a cue sheet), etc., and when all's said and done simply bounce the tracks at the bit-depth / sample rate you wish to create.
I've found SSE a
huge improvement over WL, Audition, and Audacity for managing projects with multiple large files. Shoot, even for 2-ch I think it's far better.