I just got done seperating my INtake and Exhaust Manifolds, and all the old Studs broke even though I heated them and so on and tapped on them.
Horrid old scale and irregular surfaces left on the two mating surfaces.
In my case, I had to get the Intake to be 1/4 inch Higher for it to align right with the Ports in the Head.
So, I just deleted the Heat Rise Box and Baffle, made some patches and Brazed it closed, and mounted the two Manifolds as "two" Manifolds, no longer Bolted together.
Anyway, if you remove your Intake/Exhaust 'unit' and clean the Port Faces of the Manifolds, you can Eye-Ball them to see if they are in the same plane or not, far as how they will fit against the Port Faces on the Head.
Check to see how they are in vertical positioning also, for their respective Head Ports.
Let us know what you find?
Do that first...before electing to seperate the two, since it can be a lot of work to correct things to get them back togfether again.