Although one "assumes" the manifold hole where the thermostat drops into is flat, it wouldn't hurt when the housing is off to take a true/flat block of metal or a thick file with fine surface as the base tool to wrap very fine sand paper onto, 600 grit to be safe in not scratching it up and carefully slide it back and forth without too much downward force and soon you will be able to tell as it polishes the surface, if its nice and flat or if you have a slight issue there as well. Same as was already mentioned with the glass and sand paper for the thermostat housing end of things and make sure you don't have some odd hairline crack in the housing.
Use a decent gasket ... they are not all created equal !, and I would be tempted to use a good sealer, again as was pointed out on the bolts as well but very sparingly on the gasket. Then as tempting as it is, don't even pour coolant into the engine but leave it overnight to cure completely as it sure won't hurt to do all you can to cure properly before liquid or pressure is applied. If that doesn't hold then, wow !.