A JPG has colors "compressed" enough to cause
problems. You might be able to get by with a TIF or PSD, but the scanner
needs to be used in a consistent way between when the color-checker is scanned
and the photos, themselves, are scanned.
Another thing to think about is that Tom's script
only uses three of the 24 color patches to compute the calibration so is
unlikely to be very good for very bright and dark colors. If you really
want to use a script to calibrate your scanner, you should probably use a script
more like Tindemans variation that uses all 24 color patches instead of just
three: http://www.21stCenturyShoebox.com/
But if you want to calibrate your scanner for use
with something like Photoshop, I'd suggest using a "real" calibration process
that generates ICC or ICM color-profiles that you can assign to your scans that
uses a color-target like an IT8 that has many more than 24 colors covering the
entire spectrum and brightness range.
A scanner-based printer-profiling process can
generate a scanner ICM as a side-effect.
I use MonacoEZColor which is no longer available,
to do this.
I think the ProfilePrism product from DDISoftware
may generate scanner ICM files along with the printer-based ones, although I do
not have this product so I am not sure. The website should say one way or
the other.
Once it is created, to use an ICM scanner
profile with ACR/LR you would acquire the scanned image in Photoshop,
assign the scanner-profile and then save it, then open it in ACR or Lightroom,
which will take that assigned profile into account. Depending on your
scanner software, it may also allow you to assign the profile on the way into
Photoshop, but mine doesn't, so I assign it, manually.