It reads like you built a venturi tube. If you widened the area before the MAF intake and after, the velocity of air (not just volume) moving through the MAF is going to increase. I'm thinking the MAF (being a dumb piece of electronics built for "stock" conditions) is thinking the throttle is opened wider than it actually is, so it's sending a signal to the ECM that runs counter to what the TPS is signaling. I've never seen an order of operations on these electronic ignitions so I don't know which signal takes priority, but it would be logical to think that the ECM might over correct in some way or lacking clear signals is stuck trying to figure out what's happening.