Is the SB2 fully broken in? In other word, how long has it been used since the mod? Those BlackGate and Auricaps take some time to sound good.
I'm not sure if using iTunes with Apple Lossless would contribute to the bright sound, as I don't remember that was my impression when I had an iPod and used Apple Lossless files along with EAC WAV files.
Anyway, my finding is a bit different. Compared to the SB2 (as transport)/AS NOS DAC, the SB2 analog out sounds somewhat darker. Are you comparing the CD/Ack to SB2 analog out or as a transport?
I would try to rip several tracks to EAC/WAV (really easy) and see if there's any difference. Setting up EAC/FLAC will come later, and many AC members including me can help you with that.