I've machined them both ways, and I've found it's easier to set up and machine them accurately if the manifolds are done separately. Leave the intake/exhaust attaching bolts at the heat riser area slightly loose while the manifolds are being tightened against the head, then tighten these bolts last. You're probably dealing with a badly warped exhaust manifold due to heat.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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