This is the one I made for myself. I individually converted to TTW the esm and all the esp files, adding all TTW masters (except the junk stash masters). Then I used FNVEdit to merge these plugins into Mart's Mutant Mod.esp:
Mart's Mutant Mod - DLC Anchorage.esp
Mart's Mutant Mod - DLC Broken Steel.esp
Mart's Mutant Mod - DLC Point Lookout.esp
Mart's Mutant Mod - DLC The Pitt.esp
Mart's Mutant Mod - DLC Zeta.esp
Mart's Mutant Mod - Master Menu Module.esp
Mart's Mutant Mod - Tougher Traders.esp
Mart's Mutant Mod - Zones Respawn.esp
Then I recompiled all the scripts in both esm and esp - but since the mod doesn't require NVSE I don't think it's required. Just an OCD thing :P
Then I have a slightly modified TTW_SuperMutantRebalance.esp that has Mart's Mutant Mod.esm as a master to add the scripts and actor effects from MMM to the super mutants. This plugin would be optional.
I found that I had a lot more crashes when corpse flies and skeletal decay were turned on. Now that I think of it, I don't recall ever seeing a corpse fly when it was turned on. Once in awhile I get crashes when loading into an area but I have greatly increased spawns on and hi-rez textures installed too. I believe Ghoul raise also causes crashes. So I have that turned off too.
Also, I haven't gotten around to converting all the ingestibles to hardcore friendly.