After installing a wide variety of mods (to the best of my abilities of course) and runnin them through the Boss system I cannot run the game. Whether launcing through script extender or the exe, it just crashes right to desktop.
Not using a steam version either.

Most likely you are missing a master. There is likely an esp that depends on either another esp or esm to load and since whatever is missing then the compiling of information fails and as such the game exe fails.

This is one reason why http://www.fallout3nexus.com/downloads/file.php?id=11336 is a better mod manager than FOMM - it will show you that a master is missing with bright red colors.