These steps are what you need to get the game working Post-GUTs and subscribing to it at the same time.

These are the steps, post-GUT if you don't want to subscribe Torchlight 2 to Steam Workshop.

1) Patched Torchlight 2 to latest version.
2) Went into the SteamApps/Common/Torchlight 2 folder and deleted all .PAKs file I had there with the exception of the "Data" ones. (thus made sure there was no synergies installed).
3) Once I did that, I double clicked on the Torchlight 2 shortcut in my deskstop, and the Launcher menu came up, there's 2 options Play Torchlight 2 (without Mods) or Manage your Mods and than Play after. I first launched the game "without" mods, so just clicked the little Play Button.
4) Once inside Menu Screen, this is important, don't try to start a game or load your character (it's still there from, don't worry), just simply exit out of the game now.
5) Once exited, you should see 2 new folders in your My Documents/My Games/Runic Games/Torchlight 2 area. "modsave" and "mods".
6) Simply copy, or my case "cut" (since you don't need synergy type chars in your vanilla save file) the folder labeled with all the numbers in the "save" folder to the "modsave" folder instead.
7) Once done, then go ahead and download SynergiesMod 2.006 from the site, when you open it you should see one file, a .mod file.
8. Extract SynergiesMod to your new "mods" folder in your my documents.
9) Launch Game, but this time click on the other option to manage your mods, your SynergiesMods should be shown on the left side, just select it, and it should move over the to right side as "active".
10)Once done, simply launch the game bottom Right Corner of that same mod manager window that says "Launch with Mods" (note you'll have to do this to play with Synergies, if you just click on the "Play Torchlight 2" outside of the manage Mod window, than vanilla T2 will run instead.

So there you have, 2 options, honestly the Sub route is probably easier since I think there's an "auto update" function of the any subscribed mods you have, but some people don't like to do that kind of stuff, so feel free to use either option, heh.

Salan or another moderator, I would probably sticky these instructions because they're like 3 or 4 different threads on how to get this to work post-GUTs :).