Matt,
I saw this too late to help, but I had a similar issue when taking out my pump. Some things to keep in mind: the housing is made of aluminum, so prying can be dangerous; tapping the pump with a wooden mallet is much better; the housing bolts should be all in (connecting to block) and somewhat tight so that the force applied through tapping translates directly to disconnecting the pump-to-housing joint. Once I tightened these bolts a couple taps was all it took to disconnect pump.
Regarding the thermostat, I simply attached the upper radiator hose back on to the top cover (with the housing still attached to the engine), I grabbed the thermostat cover/hose combination with my hands and yanked upwards.
Also, be careful when torquing down the thermostat and water pump bolts. Some idiot in the past over-torqued some of the bolts on mine, and ruined the threads. Now I'm having to heli-coil two of them! These housings are made of aluminum, so the threads strip easily. (and they are expensive! However, the water pump housing has the same part number across all engines of the era-- even the M130)
Even if you're done already, I hope this helps someone else!
WAQAS in Austin, Texas