Stumbling sounds like more vacuum leaks. The VAF is very sensitive to *any* leaks. Also check your plugs & cap/rotor... I've never had an alternator cause a stumbling. Is your battery light coming on? That will illuminate any time the alt is failing to charge.
For the hunting idle, it could be vacuum related. I had issues when swapping throttlebodies in the past, a poorly adjusted dashpot was causing a hunting idle for me. It was holding the plate open just a little bit, rpm's would shoot up, suck the butterfly closed, rpm's come back down, cycle would repeat. (the dashpot is the circular bit on the left side of the throttlebody, little white piece that sticks down on the throttle cam)
For your fan running constanly - is the fan switch plugged in? it's the single blade sensor on the thermostat housing. The sensor may have failed too, but I doubt the relay has failed