That being said, I'm focusing efforts on the WoD builds now - this will all change again come the patch, so it's not worth the effort of updating the MoP stuff at this point.
Thanks for the link, it's a nice guide. I've got the majority of these changes in.
I've updated a lot of the rotations ready for 6.0.2 now. Removed all the pruned abilities (like Alter Time etc), updated the talents and such. I haven't looked into level 100 rotations yet though, just wanting to get it compiling for the new patch first, then optimizing rotations can come after.
As for the under performing, there's a lot of aspects that can contribute to that. Would need to see log files and such, but as stated above, it's just not worth the effort looking into issues now when everything changes soon.