You may have heard this all before but I'm going to type it out for the newbs and it may remind you.
#1 - The thermostat housing is a pain in the arse because it only has two hold downs for the large area and it is made from stamped steel. This means that if you over torque the bolts, you'll warp the mating service of the housing. In fast the surface may warp over time just from the right torque and heat. Thus when you take it off to replace the thermostat and put it back on it won't seal.
#2 - The intake manifold is cast aluminum and has porosity. I've seen poor quality surfaces on the intake manifold and it too could be warped, but usually it isn't.
#3 - You must make the mating surface of the thermostat housing flat before putting it back on. You need a sheet of 400 grit sand paper or sheet of emory cloth on a flat concrete floor or flat bench top. Then slide the mating surface of the thermostat housing over that sand paper using even pressure. Do a few swipes and take a look. You'll notice where the high and low spots are. Keep doing that until you have no high or low spots. Clean the surface up with a finer sandpaper or emery cloth. Wash everything well after this.
#4 - If the manifold surface has porosity or is uneven I spread some RTV (for coolant, so blue or orange) on the manifold and then stick the gasket to it and let it get tacky.
#5 - I tack the thermostat to the housing by using super glue on a couple spots. Then carefully position the housing onto the manifold avoiding the gasket.
#6 - tighten down the mounting bolts only until a little pressure is felt. Then tighten them both down evenly to around 12inch lbs. It's not very much, you don't' want to force any rtv out all over the place and you don't want to warp the housing.
#7 - Let it sit over night so the RTV can cure. Check the bolts in the morning to make sure they are still tight.
Some other observations:
Felpro started making thermostat gaskets with an elastomer ring around them that solves this problem completely (assuming you don't over torque), unfortunately they don't make such a unit for our application.
Permatex makes a product called Right Stuff Gasket Maker which is essentially a two part elastomer product that comes out soft stays pliable, but sticky and can be used as a gasket replacement. I used it on a perpetually leaking AOD transmission pan and it hasn't leaked a drop since (I spent hundreds before that stuff with new gaskets, and various attempts). If I was serious I'd try it on the thermostat housing. Only downside is the stuff is a pain to clean off. It's tough stuff.