THe 454 mpi was not running right, down on power and missing last fall when I had it winterized. The other day I pulled the stainless marines off to put them on the new motor and there was a little water on in the bottom of the runners. would running crappy/ missing make it revert enough to cause this?

Today I got the fittings to hook the manifolds to the hose with the outlet plug, so the manifold was under city water pressure.. let each sit for 1/2 under pressure and neither showed any signs of leakage...

a tired engine with weak or broken exhaust valve springs will cause a bad valve to seat seal,this can cause reversion.not saying this is your issue.how many hours on this engine.

Unknown hours on the engine, though it does have quite a few hours with the throttle bungied to the dash.
The motor was running decent, taken out of the boat, sat for a year and half...thru it back in the boat to test the new x dimension (while waiting for the new motor to be finished) , first time we tried to take it out, it had a bad stumble, and wandering miss, wouldnt even get the boat on plane... Being the end of the season I just had the local marina winterize it. it defininitly wasnt idling all that nice while it was getting winterized.