You can probably get Q3 to work at a lower resolution (if you want) by adding that resolution to the end of the Modes line that you're using. So the Screen section would look something like:
# other lines here...
Modes "1024x768", "800x600", "640x480"
# more other lines here...
Where the comment lines would be replaced by whatever else is currently there. The important thing is to have multiple resolutions on the Modes line in question.
As for the mouse, I have no idea. I haven't played Q3 myself, ever, so I don't know if that config file is set up right. Your InputDevice section looks OK, though, plus if the mouse works in everything else, I don't think the XF86Config is the problem.
When you say the mouse "doesn't work", what do you mean? Does it not move at all? Is it erratic? Does everything but the wheel work? Again, I may not know what the problem is, but there might be a couple of things to look at if most of the mouse works.