At my shop I had an exhaust manifold stretcher I think you can buy them still ! Your manifold didn't shrink it warped and its common! Usually the studs brake or come out very tight when removing the manifolds because they were warped while on the engine Before tear down, and it isn't noticed by people till its assembly time! You should have them machined flat too sometimes there is a twist with the warp that wont let them seal!
My tool is a "Lyle 31000" exhaust manifold spreader