When you took the water cooler out of the intake manifold, you just cut a square in the front, pulled it out, and patched the hole? Are you positive there isn't an obstruction inside there that's blocking one of the throttle bodies from flowing?
I would reconnect the front of the intake pipes to the supercharger, and then disconnect the intakes from the throttle bodies. With the supercharger blowing, you should see some voltage on the mafs. If they're still unbalanced, your problem is in the intake pipes or MAFs. If they are balanced, then it's an obstruction in the throttle bodies or intake manifold. At least it would give you a direction for where to look.
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