Ripping to a Mac, any software?

Are you using an external DAC?
If you are using an external DAC,
are you controlling volume with
the iTunes user interface, or with the DAC?
If an external DAC, what interface are
you using between the computer and the DAC?

You might find it best to defeat the iTunes
equalizer altogether: un-click checkbox on equalizer
widget top left.

Importing directly to iTunes, error correction 'on',
Apple Lossless, will give you bit-for-bit at playback.
*All other things being equal*, your music server should
sound exactly like a transport. Mine does.

Heymikey, so you've got some top-notch gear there all-around.
I don't know, but it's fun guessing, and my first guess might be ...
I wonder if you might be losing anything in the Mac-to-DAC
USB to SPDIF converter. Just a guess,
my experience has only been with USB all the way:
Mac to Bel Canto DAC3 USB port.

I don't think the hard drive makes a bit of difference,
as long as it's not junk, and noisy -- in the same way one USB cable
is just like another, save maybe better fitting ends.
It's all bits in both cases.