As for the MKs on weapons, this is an important point that aaaict points out. I'm using MkXIVs now so my DPS reports have been based off of them, but over the weekend, I had a whim to take a look at the new Kelvin timeline beams so I bought some and loaded the ship up just to try them out. They were all XII, but I wasn't interested in putting time into upgrading them if I didn't like the looks so I joined up for a fleet action and gave them a spin.
My DPS was nearly 1/2. Between the difference in Mk XII and XIV and the loss of the % to crit I get on my Fleet Anti-protons it was a huge difference.
On the bright side...hitting at or near 10K with MkXI or XIIs means that when you get them upgraded to Mk XIV, you'll shoot passed 10K with ease.