Truck runs rough and shakes. So far I've changed out the plugs/coils and cleaned the MAF sensor. My scanner showed normal MAF values at idle and 2500 rpm. However, I don't know much more about scanner stuff to determine the problem. I found these two cables and I don't know if they should connect to each other or what?

 

Thats two ends of a broken vacuum line, I cannot find a diagram for how the vacuum lines are routed on this year model though.
You can look all around in those areas for the other ends of the broken vacuum line is, keeping an eye out for wire loom that does not have any wires coming out of it.
If you do find the other ends and do not want to replace the entire vacuum hose harness(for lack of a better word) you may have some luck getting flexible vacuum hose that can be slid over each end of the broken hoses to repair it, this will have to be a very tight fitting hose and you may need to put a little lubricant on the outside of the hard hose to slide the soft hose over it.
If might help others if you would state what engine you have, I do not know if the vacuum house routing is different for the two engines.

 

Update: I found these two lines are the vents for the IWE and are not supposed to be connected to anything. I'm going back and double checking all vacuum lines and I'm thinking about buying a smoker to see if I can find a leak anywhere.

 

If you traced where each end of that vacuum line went ,you would have a pretty good idea of where they go and what they control.