A couple "tricks".
a. Clean up the manifold sealing surface so it's shiny. A hard rubber sanding block with some #180 emery paper until it's uniformly flat. Glue the emery paper to a scrap piece of plate glass afterward and slide the thermostat neck across it until that surface is flat.
b. Take a rubber band and loop it through the "cage" on the thermostat, then feed the loose end out the thermostat water neck and loop it again over the outside of the neck to hold it firmly in place, then, using some Aviation Form-A-Gasket, glue your gasket in place and let it "set up" a bit before installing. Also apply a thin film of F-A-G to the bolt threads. When installed, snip one loop of the rubber band and pull it out.
PS: The heater outlet is fine, although I'd bet that one has no restriction inside and I'd want one with a 3/8 hole inside or put one of these in the end of the heater elbow before attaching the rubber hose....
Everbilt 3/8 in. x 5/8 in. x 1 in. Bronze Flange Bearing 838638 - The Home Depot