Water pump replacement?
 

Okay, in replacing my water pump I noticed what appeared to be a broken bolt. I went to use a tapout to get it off. I finally just drilled it out to the edge of what I needed to get it off. Afterward, I realized this bolt came in from the back. I just left it out as I went back together. I noticed I had some extra gaskets and an o-ring I wasn't sure where they went. I finally figured this out by looking at the schematic where they all went. I was supposed to pull this entire assembly out. Looking at other photos of WP replacements I hadn't seen anyone else do the job this way. Has anyone else ran into any problems not pulling the back mount off or leaving the one bolt out? I waiting on some parts to go back together so I thought I would check before going too far back together.

You need ALL bolts. If you pull on the rear housing it will pull off and that's where the oring goes. All gaskets should have a place there. You mayaswell change the timing belt as long as your that far into the motor...EASY to do. Mind your torque specs and the fuel rail is 9 lbs. Not 106 lbs.

I learned some things while replacing the water pump I didn't see anywhere else here and thought would be worth sharing. First, these are two of the three bolts you are expected to remove in replacing the water pump. However, the back bolt in the picture is beneath the lower intake plenum and near impossible to get to.
http://imageshack.com/a/img540/8100/tUDKV3.jpg
However, in this second picture, with the lower upper hose removed, there are another three bolts that are easily accessible which will have the same effect to remove the water pump. This gasket isn't included in the kit and the other one is, so I just reused the metal gasket that was already installed and I will watch to make sure there are no leaks. It will not be hard to get to should it develop a leak.
http://imageshack.com/a/img673/7129/REUEC7.jpg
By removing it completely, you can replace the back gasket and o-ring and access the screw/bolt, which I mistakenly thought was a broken bolt and tried removing with an extractor. You can see in this pic my shiny new screw/bolt which is a little longer than was needed.
http://imageshack.com/a/img673/8831/Pr0uvp.jpg

Would it be easier to remove the water pump and thermostat housing together and then separate them on the bench?

Hunter that's what I did with my water pump and it worked out very well that way.

HunterD, yes, you can easily do it that way. I replaced the thermostat before I realized I would have to remove the whole water pump assembly. Either way is no issue.