Sounds like you've really been working hard to improve your system. I've really been enjoying the PWT/PWD combo myself. Are you using PS Audio's silver HDMI yet? I've heard its really good.
I've used the following tweeks to my Perfect Wave combo. I have found that placing 3 Mpingo disks on both the transport and DAC really made the combo sing. Other tweeks have been Herbies Tenderfeet under the transport placed as close as possible to the factory footers and to the right of each. The DAC didn't seem to like this arrangement so I'm now using 3 Vibracones two in front and 1 in back (middle). I'm going to have another group of tenderfeet sent out to try with the DAC.
As for the HDMI cable, I started with a Nordost (don't remember the model) and am now using a Signal Cable HDMI.
I'm hoping to try the PS Audio silver HDMI in the near future.
For powercords, I've tried the stock, Synergistic Research, Signal Cable Digital, and VH Audio Flavor 4.
Of these the VH Audios seems to be the one to use in my system. The bass gained more impact and was more transparent.
What tweeks have you tried?
I've also upgraded my system since we orginally started discussing the PWT/PWD.
Enjoy your system.
Steve