We had this problem on cast iron manifolds on an SBC once. All we did was get long studs and slowly threaded the manifold on until it was straight and flush. After it was against the head, we swapped the studs out for proper bolts and called it a day.
A friend of mine used to race circle track and he said they would do this all the time. The heat just expands the metal and causes it to warp when removed because there is nothing holding it straight.
good luck