my experiences:
1 & 2)
-anytime i modify a ui file the whole ui gets scrambled to defaults
-all my windows stay where i put them unless i change an xml file
3)
i closed the pet window the first time i saw it and have never seen it since. but try this:
in the main eq dir there's a config file called
UI_CYMORG_##.ini
the ## will be your server number, but who cares. in there look for
[PetInfoWindow]
XPos1024x768=50
YPos1024x768=304
BGTint.red=255
BGTint.green=255
BGTint.blue=255
Fades=true
Delay=2000
Duration=500
Alpha=255
FadeToAlpha=128
Locked=false
Show=0
if show=0 then, by default, the pet window won't show up.
same thing for the window selector, which is right on top of the pet window