Every time I launch the game from the script extender, the log file keeps popping up which messes up the game a bit. It makes the desktop clips in the game, so I have to semi-blindly click the stupid log file in the game to close it out. Anyone know how to prevent the log file from popping up?

EDIT: Okay, I think I fixed it... It only seems to happen if I load the game from the script extender without opening the original launch first. Is that why I was told to check the mods in the original launch then launch the game from the script extender?

use the mge-included.

How do I use that?

It is a third-party program like MWSE that additional boosts your graphics. There is a thread hanging around here.
Download: http://sourceforge.net/projects/morrgraphext/
Installation: http://sourceforge.net/apps/mediawiki/morrgraphext/index.php?title=Installing_MGE_correctly
Thread: http://www.gamesas.com/index.php?/topic/1204129-morrowind-graphics-extender-mge/