Bob,
You have done everything perfectly. If the intake manifold were to grow with temperature, the head would grow too, so it's a wash.
I haven't used the thick gasket, but it might be the ticket. I have always had the combo machined flat and stuck it on with no problem. Starting fluid is pretty high powered...could your increase in RPM have been a result of some of the concoction finding its way into the carburetor versus a true leak?
If the assembly is truly flat it will seal. If it is warped a tad, the fat gasket, plus all the rest of your great work should pull it flat. Good luck.
Stuart
