Had to boot back into recovery (clockwork seems to have dissapeared again...) wiped data/cache in their and now everything appears to be working again.
Now I just need to root it....
This seems like the easiest way to root it following this guide:
http://samsunggalaxysforums.com/showthread.php/4563-root-the-Galaxy-S-II-via-SuperOneClick
But I'm wondering will the XWKDD kernel used in that guide work for my phone even though my Kernel version is BOKF3? I think this is the issue I had yesterday, couldn't root it because their didn't seem to be a BOKF3 kernel.
Cheers
OK so get unsecure XWKDD, Flash with Odin once booted use superoneclick to root, then flash back to normal kernel & check with root checker app you are rooted.
That is the method I did when I wanted to keep stock & root. Do you not have BOKF3 stock kernel? What kernel did you just flash?