Hi. I tend to screw with my load order every other time I load up Fallout. For instance,

Character 1: Arwen's Tweaks, Fellout, RI, Zumbs.

Character 2: FWE, Xepha's weather, missing unique weapons

Character 3: FOOK

Yes the lists are very long for each one, and I don't feel like checking and unchecking dozens of mods each time I play.

So I went into GECK and attempted to pile them into one huge .esm

Didn't work. So, help?

I'd suggest you to use garybash.
With it, you can save your load order (and activated mods) and restore that setup anytime you want. Of course you can define multiple setups.
http://www.fallout3nexus.com/downloads/file.php?id=11336

be sure to follow the install-instructions.

That really isn't a very good idea. If there's any sort of conflict then it's going to be a nightmare trying to isolate the problem. And if there's ever an update to any of those mods, then you're going to have to go through all that hassle again. Merging mods is not something that's easily done. FWE works because the authors put a great deal of effort into making everything compatible.