IIRC there is a 1/8" variance allowed (anyone confirm this?) on the runners but the heater must be flat as well as the intakes stove underside.
1/8 inch warpage seems like a lot, the stock gaskets could not seal that, with that much warpage I would think the sealing of the intake manifold to the head would be compromised. I don't deal with stock style exhaust / intakes, but I would think that flatness no greater that .030 would be max. The manifold flange faces are more critical to noise and engine performance than the stove faces....