Hmmm, strange one.
If, and I'm only plucking thought out of the air here, the manifold hadn't seated tight and there was a leak from around the manifold, what effect would this have on the engine Bill? This would effectively be the same as having an induction leak???
The car may have run OK initially, but as it got up to temperature the strains on the engine will have increased as it got up to temperature. The engine will build up its compression, and will exploit any gaps between the manifold / gasket / head.
Could this cause this kind of behaviour, or would the engine not run at all given this kind of scenario?
How painful is it to refit the old manifold in hours. I think its the only way to see if its the manifold at fault. Could you get hold of a new gasket for it before the automotive shops shut?