Ok I ran a few tests with both sets and here's what I found:
1) Installing the _SOEp7_mainhud_pet.xml file included with version 3.4 does in fact resolve the pet button issue. I suggest everyone install this version of the pet window, even if you don't use a pet. It could solve some other problems that might result from loading the old command buttons.
2) I tested every Market window search option and everything (including the new menu) works as expected.
3) I was able to start a group just fine.
4) Zoning did not result in any problems.
5) Quest windows appear to be working normally.
6) I wasn't able to test the choice window, but don't expect any issues.
7) You shouldn't have TooltipStyles in your custom UI directory in the first place, if you do, trash it
8) I'll need to update the Questionnaire page at some point, but have never seen it actually used for anything. The missing "Don't Care" option for each question shouldn't cause any real problems.