The fading can be done globally in game (although it will reset everytime you /loadskin). Open up all the window you don't want to fade (including all bags) then press ALT-O to bring up the options screen. Under Display there are 2 sliders on the bottom right. These 2 sliders (forgot their names) control the transparency of a box in normal and faded mode (top being normal, bottom faded). The sliders on the left - the top one controls how long a box stays in normal mode once the mouse leaves it, the bottom one controls how long in seconds it takes the window to fade from the normal transparancy to the faded one.
The buff window with the words on it. If you look at my (Geddines) buff window on
www.eqinterface.com it has a shrunken icon with the text beside it. If you look around you'll see many have made changes to this window even to give it a look they like. Some say it is slightly bigger than they like, so I hope to come out with a smaller version soon.