Only reason I can think of FTPiiUEverywhere not working for me is cause I use Haxchi instead of Mocha.
Anyways, I too tried modding the update file and noticed when NUSPakcer packs it, it doesn't pack it correctly. Only a few kb when it should be about 1gb.
I tried modding the base game, but an update is required to even play it. I installed the update (unmodded, like I have a choice) and it completely overwrites my mods, making the fact I modded the base game pointless.
I just tested it with Loadiine. The game loaded, but as soon as I went to change my skin, the game crashed.
Why does Minecraft of all things require so much work to mod? Might as well just buy the PS3 version since it's as simple as copy and pasting a custom pack into the DLC folder...or I can try finding a reliable crack of the PC version, but I won't have split screen (hence why I'm focusing on consoles).