Also how tight does everyone torque the thermostat housing studs? The Haynes manual says 20ftlb but that seemed excessive to me
I'd just snug them down. As for the remaining water in the system, I'd pull the block drains and blow out (or shop vac) the heater core. Don't beat yourself up over getting every drop of the flush water out.
Are you using premixed or concentrate coolant? Concentrate is cheaper, distilled water is cheap. Using concentrate will give you more control over the coolant mix your running, especially if you still have some straight water remaining in the system.
Since the thermostat is already out, I'd fill the block there up to just below the housing then install it. Doing so reduces the chances of trouble with bleeding the air pockets out others drill the t-stat to address. (I've never drilled one, had cracked a t-stat loose to bleed air in a hurry though)
Probably goes without saying but, when you fire it up after filling, keep an eye on the temp guage as well as for leaks.
FYI, the factory service manuals are available on this site for download in the engine forum as a sticky.