I have never come across this problem. But I will put in my 2 cents anyway.

The MC18 runs a ratio of about 30:1 when the oil pump is being used. So I would tend to want to run that ratio,.. at least initially.
You say:
"Engine does seem to have lost any power", but I guess thats just a typo and is supposed to be,
"Engine doesn't seem to have lost any power", yes?

I assume that the "cold" pipe is still pretty hot. I also assume that you are now running two pickups for the PGM-II, and have good spark on both cylinders.
So perhaps the difference is due to the carburation being quite lean for the hot side and quite rich for the cold side? Try a plug chop when you get it mobile maybe?
Or maybe the "cold" side has a blown base gasket, main seal, or leaky reeds or something like that.
Perhaps a compression test might show a lower compression on the "cold" side?

But you state that "the engine doesn't seem to have lost any power" (assuming typo), so maybe I have got it all wrong?
Perhaps it could be something to do with the way the water flows through the cylinders and heads? From memory, the orientation of the head gaskets can alter the water flow slightly? Maybe it has something to do with the water pump?

Just throwing ideas out there. Hope it helps, or at least triggers someone else to add their thoughts.
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