Why do you want to do a flush? Unless the coolant is visibly dirty, there's no reason to do it. I'd just drain the system completely, run a little bit of water through it (with the engine off) and then refill it. I don't know about taking out the thermostat or running the engine while flushing it, I always get nervous about localized hot spots that could crack something. Be sure to fill the block through the upper radiator hose first and only when the engine is cold! Also don't dump any of the coolant, even if it's diluted, onto the street. It seeps into the soil and ground water and it's extremely toxic.
If you didn't already know Zerex G05 is the same thing as MB coolant, but it's cheaper.
