1. Definitely sounds like an in-game option or something that you missed. Can't be sure really. You could try backing up and deleting your eq2_recent.ini before going in to game to see your results.
2. EQ1 has custom in-game sound triggers. Unfortuantely EQ2 does not. There's just no way to parse chat with the UI, especially not "sub strings" of chat. With enough feedback, maybe this could get added one day...
3. A lot of windows that you can set Click-Through on, you can still interact with the window, you just have to either right click specifical elements or left click buttons. Some window seem to vary with this. Personally I play just fine with most windows and click-through successfully enabled. I play with the keyboard a good bit, just to note. If you learn to turn your screen with a combination of both your mouse and your keyboard, you'll only need to use certain parts of your screen. I personally am comfortable with panning the camera up and down with keys to avoid clicking windows, as well as using both left and right mouse clicks to move the camera or my whole character.
4. The biggest thing with tab targeting is being in combat, and also with creatures in an "encounter". If you are incombat with an encounter and you try to "tab" through them, you'll always stay in that encounter. Tabbing always picks up where it left off (unless you get taunted). The best way to tab to newly aggro'd creatures is to target the closed NPC (keybind Target Nearest NPC) and then if needed start tabbing through the targets. But like I said, if you're in combat with creatures in an encounter (more than 1 mob), it's just gonna cycle in that encounter. I don't use the Tab key specifically, I have my own hotkeys, but do what is comfortable with you. Maybe set Tab to Target Nearest NPC, and Shift+Tab to cycle through them.
5. Just how it is. They're probably using some sort of javascript in the Copy buttons and it just doesn't work in the in-game browser. Not much we can do. Can try asking on the forums and hope for feedback, but I doubt it'll ever get high on the list.
6. I played in windowed mode and just stretch the screen out. If you are bent on totally hiding the title bar at the top^, then you can mess with your eq2_recent.ini and messing with the location/size of the window. See specifically for example:
cl_screenwidth_windowed 1675
cl_screenheight_windowed 1022
cl_screenposx_windowed_restore_down 3
cl_screenposy_windowed_restore_down 24
And lastly, as for the target window constantly auto-resizing the effects down, you would have to create an OnSize property that constantly sets the effects to a static "x,y" width and height. I can't give a more forward suggestion at the moment as I don't have the time to look at the code and give a proper size estimate.
I'm glad you have come up with a UI setup/layout that works for you and makes your game experience a better one. I think how we interact with the game is one of the more important things in the grand scheme. Hopefully Sony will continue to invest time in the UI features in the future.
Hope all that helps. Cheers.