Well... you checked the wiring, and that looked good, and you replaced the sensor so it HAS to be clean. And you patched the holes in your intake tubing. Sounds like you did everything one would normally do.
Did you check your air filter? Sometimes a low MAF voltage can be caused by it simply not reading enough air-flow going through... or Maybe something is stuck in the ducting blocking the air flow... perhaps before the filter, like some leaves in the resonator behind the bumper or something.
It's could be a faulty computer as well... but that is HIGHLY unlikely. Did you try to disconnect the battery for a few minutes to give the computer a chance to loose all it's saved settings and therefore needing to relearn everything after the "first" start up?
Also how does it drive. Does it feel sluggish or not as peppy as usual? And how does your MPG look?