I just listened to that section on my 192/24 stereo version (from the HDAD DVD, which was the basis for these adjustments) and then on my remastered 5.1 and aside from the fact that the 5.1 is a bit more compressed than the stereo, they sound almost identical to my ears in terms of tonality.
It's hard for me to diagnose because I don't use Audacity and I don't know exactly how you've converted my EQ curves into Audacity EQ curves, but you may want to re-check your calculations if it sounds that objectionable. The only other thing I can think of is that if you haven't reduced your preamp/input volume prior to the EQ, then your adjustments are pushing the peaks above 0dB and causing clipping. As you can see from my list of adjustments I had to reduce the volume of Nothing Left to Lose (Track 9) by 3.9dB before feeding it to the EQ plugin to avoid clipping.
I dunno if anyone else has undertaken these adjustments (
@MrSmithers mentioned to me that he was going to try, but I'm not sure if he did or not) but maybe someone more well versed with Audacity could chime in.