Ignore everyone else and listen to me: I have had this scanner since shortly
after it was released.
The issue of color management is a non-starter: there is an ICC profile for
the scanner and if you are that serious about these issues you already or
will develop a color work flow routine in Photoshop where color management
belongs, not in the scanner software. Any truncation of the exposure
information done in the scan software, such as adjusting levels or curves,
loses information for processsing in Photoshop.
In reality Vuescan, which I have, offers absolutely nothing over the Canon
software if you are going to process your images in a decent program like
Photoshop or Photopaint. Vuescan does not interact with the FARE
dustcleaning system properly anyway.
Silverfast is now offering software for this scanner: however I personally
have not found the demo justifies the $200 cost.
If the scanner is directly connected to a USB port and does not pass through
a USB Hub the scan times are only slightly longer for USB than SCSI. But
this scanner is slower than comparable Nikon models (it is also much less
expensive).
There is NO difference in "noise" between the SCSI and USB connectors.
This scanner does an excellent job with APS if that is a significant
consideration to you, although the mechanics of using the APS adapter make
scans slower than with 35mm materials.
You will rarely scan above 2400dpi if you do not plan to make prints larger
that 8x10 inches. 4000dpi yields a 50-60mb file, I shudder to think what
5400 dpi yields. When you print whatever software you use is going to
discard most of those pixels anyway.
Whatever you do make sure your computer has at least 512mbs memory.