I recently built a seemingly high end PC, and it's running Skyrim absolutely awful.

Specs are:

CPU: AMD FX 8350 8-Core Black Edition

Graphics Card: Nvidia Geforce GTX 660 ti

16 GB Corsair Vengeance RAM

Motherboard: ASUS M5 A97 R2.0

I've tried running it on ultra... forget about it.

Tried running it on high with shadows on low... it runs ok when I'm walking through towns but loading times are minutes long, and it starts to grind when a battle starts.

Any idea why it's running so poorly? AMD? Should I have gotten a Phenom II?

Using the game or the Nvidia control panel to set AA? Hint, use the game's settings.

Have you disabled the Gamepad and Rumble in the INI and Prefs files? Both in My Games and the Root install directory (Prefs may only be in My Games) That won't affect loading zones but it will reduce stutter issues.

Are you running any mods or is this a fresh install still?

I've got about 20 mods running.

Also on average, I'm getting 4 fps...

Use BOSS if you haven't so you can see if the load order is just wonky, or if there are dirty edits in some of the mods.

Tried it. Didn't help. Also tried it with no mods. Nothing.

Have you made any changes to the *.ini files - ugrids for example ?

Did you try the suggestions made by CCNA ?

Yep and yep. I'm wondering if it's because I'm using two graphics cards... I have the GTX 660 Ti in the secondary slot, and an older one in the primary slot that my monitor is plugged into.