Perhaps I'm wrong, but main thing the OP needs/wants given the features in OS X 10.4.x is focus follows mouse in Terminal? (Bear in mind I've only skimmed the article; too many out of date or easily resolved complaints to read it properly.)
iTerm has a 'focus follows mouse' option in its preferences (off by default), try using that. It also has tabs if you prefer less clutter.
My installation of Terminal on OS X 10.3.9 has focus follows mouse, but its gone in 10.4.x. I've asked Apple to add it as a preference; if others join in and give feedback it'll probably happen (the code to do it is obviously there).
IMHO focus follows mouse has less value outside the command-line, although I can see some value for editors, etc., that dominantly work through keyboard input. It also introduces a nuisance; if you move the mouse to get the pointer out of the way of your typing, you have to be careful where you put it or you'll divert your typing someplace else (heaven knows I did this often enough in Terminal in OS X 10.3...!). The result is that a lot of time is spent "being careful" with placing the mouse. I'm not surprised Apple has avoided focus follows mouse as it'd rattle their main user base (old time Apple users, newbie consumer users; developers are only subset of their market). I'd still like to see it as a preference in Terminal, though.
For domininatly GUI-based apps, there is much less value in focus follows mouse. E.g. in Finder the needed actions (dragging items, etc) already work between windows and for textboxes, etc., you want to select them first or you'd have be to incredibly picky about where you "left" your mouse pointer given GUIs are full of small input elements.
Incidentally, setting 'Preferences>Windows>Select windows when mouse moves over them' in Fedora 3 doesn't change anything... what's with that? Personally, I'd rather pay a little and have my time dealing with my client's solutions, not fiddling around fixing in-house issues which are just another overhead. That said, Linux is an excellent server/developer platform.