First off, try to keep images down in size or have thumbnails to click. Having large images like that will also increase the width that the text can use making it a little hard to read everything.
1) Doing a search for tooltip addons should give you what you're looking to do. You can try
TinyTip and see if that's to your liking
2) For buffs/debuffs, it's personal preference on what you'd like to use.
3) Are you talking about the frame of the Quartz bar or the color of the bar itself? Type /quartz to bring up it's configuration menu.
4) Pretty sure that you can't have regular actions and abilities on AutoBar. It was meant to help save space on your action bars by taking consumables and such and putting them there.
5) I don't have any experience with eePanels so I can't help you out on this one.
6) I haven't messed around with the configuration of Prat, but I'd assume that any chat windows that you create will be covered by Prat. If that's the case, just create the windows you'd like!
7) While I'm using Fubar now (I'm using MazzleUI) I haven't played around with any of its settings. Bring up it's configuration screen and poke around in the settings.
8) Check out
OmniCC for your CD needs.
9) Try
Cycircled (direct download link) and some of the skins (found
HERE at the bottom of page 3) for it to achieve your glossy look. Not sure if it's compatible with InifiBar or not though...
10) For the PitBull buffs, you should be able to change their positions within PitBulls options.
If anything I've said is incorrect, please feel free to correct me! I don't claim to know a whole helluva lot about the addons.
One thing that I personally would change is the stacking of your clocks (I'm assuming local and server clocks?) and your status window. I'd have them be in a line so that you don't have that awkward looking space between your action bars and AutoBar. That'd allow you to get a full new action bar in that spot if you'd want one.
You have a pretty nice start to a UI! First and foremost remember, it's yours! Tweak it to however you want! For the people who criticize, pay no attention! For the people who leave comments about elements of your UI, take them if you choose (you won't hurt my feelings if you don't use my suggestion!). Some comments may make you thing 'Why didn't I think of that' while others will make you think 'WTF were they on when they said that'. It's how it all happens. I'm sure with the fixes you're looking for and some tweaking yet to come, plenty of people would like to download and try out your UI.