As I only had 3 panels in my UI setup, I upgraded to the new version and found it pretty buggy. After creating 2 panels and tweaking some global settings, I found that I was unable to create a new panel using the global settings. Or rather, the panel wouldn't show up. Creating a panel using the default settings caused a new panel to appear. Doing a console reload removed all ability to edit any of my existing panels; they simply didn't show up in the menu (Fubar or Waterfall) for selection. I deleted my WTF files & eePanels folder, reinstalled it, and the same thing happened.
Out of curiosity, why are you not releasing this major rewrite as eePanels2? I reckon a lot of folks who don't read these forums will be pretty upset when they update via the WoWAceUpdater only to find their entire setup erased. Having the rewrite as a separate mod would let people update as the stability & functionality is proven superior.