If the internal resampling and dithering in the Alesis is high quality, and I'm sure it is, then it would probably yield results that would be indistinguishable to most ears vs. resampling and dithering with a PC software program. However, I think Wavelab is the best program for dithering. It has Apogee UV22HR dithering, which is the best I believe. r8brain is a very good free sample rate converter, but I think the pro version of r8brain (not free) is the very best available for resampling. Not that it makes too much difference, though. The folks who really care about sound quality will want the 24/96 audio, and pretty soon most everyone will be listening to 24 bit audio if it is available.

For the analog reels and cassettes, it would be good to transfer it as few times as possible, as I have read that every time you play back a tape, the sound quality degrades a little. So it would be ideal to transfer a tape once at 24/96, then archive the 24 bit raw files, then edit the 24 bit files if necessary (tape flips, patches) and archive those, master and process the 24 bit files if necessary (I think only engineers and experts do this though) and then archive those, then make a CD quality version from the edited, mastered files by using software conversion (on a PC or Alesis type deck), then put it on the shelf until 64 bit A/D converters are introduced.