Congrats on the new rig, Bram! I know the feeling of going into downtown Boston without any stuttering.
And though I'm a little late to the conversation (work has sucked out loud lately), I use Mod Organizer II. It also has LOOT built right in, and though it took some time to get used to the setup and file structure, I really like it, especially for putting together my own custom mods. The biggest difference is that it doesn't mess with the native Data file in the game. It keeps every mod contained in its own cozy little file structure, and it's easy to use LOOT as well as sort stuff around on your own. It also has decent documentation.
I wouldn't recommend doing it for a current game. It's possible, since I did it, but it was a pain in the ass to get my current games up and going. I don't think I'll be trading it anytime soon though.