I'm modifying a theme (ClearONE), and have moved the tray from the bottom to the top of the screen. However, now the icons are too low in the tray. I read through the xtray docs, but couldn't find anything that dealt with where the icons are placed in the tray. Any help?

Oh! Same problem with the clock, which I also moved. However, I don't know which module is responsible for that.

It probably has to do with the xtray borders. Scroll down in the readme and check out xTrayBorders, and find the corresponding setting in the theme. Can also be set as xTrayBorderLeft/Right/Top/Bottom.

The clock is probably a label. Look for something like "(LabelName)Text [time]" and check out its borders.

(That's off the top of my head. I don't use that theme.)