I'm playing the PC version for the first time as I want to try some Mods but after well over 600 hrs on the 360, I just can't get used to the keyboard and mouse configuration, is there anyway to use the 360 controler on my PC?

You can try mapping some controls in game, but they don't work well. You can also try a 30-day trial for Pinnacle Game Profiler for much more control on mapping.

I'd recommend just grinding your teeth and get used to the keyboard and mouse. Once you do, you'll wonder how you ever gamed without 'em.

What difference is there between remapping ingame or using that program, also does it allow the 360 controler to be used on my PC, the site wasn't clear about that?

Not all games use gamepads properly, or even allow it in some cases. With a third-party program such as Pinnacle, you have more options and control on how the controller behaves, such as the sensitivity of the sticks and triggers.I believe you can even set up macros so that pressing one button on the controller will set a hotkey, such as a spell, and immediately cast it. I can't say for certain, since I never use a gamepad with this game, but I've heard some pretty good experiences with Pinnacle.

As long as your 360 controller has a USB connection, it will work on Windows.