If anybody could help me clean up my load order it would be much appreciated. I recently used the installation cleaner after not playing for quite some time and installed FWE with MMM and WMK. I get CTDs on startup now.

Fallout3.esm
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm
CRAFT.esm
CALIBR.esm
FO3 Wanderers Edition - Main File.esm
Mart's Mutant Mod.esm
MyMansion.esp
CRAFT - Activation Perk.esp
FO3 Wanderers Edition - Main File.esp
FO3 Wanderers Edition - DLC Anchorage.esp
FO3 Wanderers Edition - DLC Broken Steel.esp
FO3 Wanderers Edition - DLC Mothership Zeta.esp
FO3 Wanderers Edition - DLC Point Lookout.esp
FO3 Wanderers Edition - DLC The Pitt.esp
FO3 Wanderers Edition - Followers Enhanced (BrokenSteel).esp
WeaponModKits.esp
WeaponModKits - FWE Master Release.esp
WeaponModKits - OperationAnchorage.esp
WeaponModKits - ThePitt.esp
WeaponModKits - BrokenSteel.esp
WeaponModKits - PointLookout.esp
WeaponModKits - Zeta.esp
Mart's Mutant Mod.esp
Mart's Mutant Mod - DLC Anchorage.esp
Mart's Mutant Mod - DLC The Pitt.esp
Mart's Mutant Mod - DLC Broken Steel.esp
Mart's Mutant Mod - DLC Point Lookout.esp
Mart's Mutant Mod - DLC Zeta.esp
Mart's Mutant Mod - Feral Ghoul Rampage.esp
Mart's Mutant Mod - Hunting & Looting.esp
Mart's Mutant Mod - Increased Spawns.esp
Mart's Mutant Mod - Natural Selection.esp
Mart's Mutant Mod - Tougher Traders.esp
Mart's Mutant Mod - Zones Respawn.esp
Mart's Mutant Mod - FWE Master Release.esp
Fellout-Full.esp
Mez's Merged Patch 5-0 - DLC-FWE-WMK-MMM.esp
xCALIBRmunitions.esp
ZL-ACRForFWE.esp
OMFG.esp

CTDs on startup means you're missing a master.
Either load your load order up in FO3Edit and it'll let you know what exactly is missing a master, or disable your mods one by one.

The MMM, WMK and FWE files look to be in order, you should only remove all the following files because they are included in the FWE MMM menu:
Mart's Mutant Mod - Feral Ghoul Rampage.esp
Mart's Mutant Mod - Hunting & Looting.esp
Mart's Mutant Mod - Increased Spawns.esp
Mart's Mutant Mod - Natural Selection.esp
Mart's Mutant Mod - Tougher Traders.esp
Mart's Mutant Mod - Zones Respawn.esp

You should probably try disabling these three first and see if that helps.
xCALIBRmunitions.esp
ZL-ACRForFWE.esp
OMFG.esp

I got rid of the optional MMM files and still had a CTD, so then I tried the last three files and narrowed it down to xCALIBR. Is there any compatibility patch for this and FWE?

I didn't say removing the above files would fix the CTDs, I ment you should remove them because you dont need them.

And xCALIBR and FWE work fine together, like I said you are simply missing the master file, namely xCALIBR.esm

Yes I know, I just didn't realize they were included in the new FWE version. And ah I see, I didn't even think of that even after you mentioned I may be missing a master file for something.

Thanks!

Ah, now I'm having issues with the xCALIBR munitions shop itself. Rather than make a new thread I'll just post it here.

All of the meshes seem to be missing (those big red exclamation marks are everywhere throughout the shop and the sign outside is also missing) as if I didn't install the meshes. However, I did, and I tried reinstalling all the meshes/textures and still got nothing.