Some causes of hunting idle:
MAP sensor. If you get a new one from GM, You will get the newer replacement which is the same one used on the early 90's V-8's which seems to provide a more accurate read.
Vacuum lines like the hard plastic ones that run under the plenum can split and cause a leak. The EGR tube could have cracked or shifted during the trans swap causing a leak. If the TB was removed, The IAC tube that runs from the backside of the TB to the lower intake could be leaking.
If the IAC is dirty, even disconnecting it will not affect it. The setting is set by the ECM once you drive at 40mph and it will always reset to that point.
Once you clean it out your idle will run high, Just drive it and the ECM will then reset it.
Recheck the electrical connections. You could have dirt/corrosion in one of them especially if you had it apart during the swap. Radio Shack sells Contact Cleaner, Since it happened after the swap, I would clean all connectors that you had previously disconnected, as well as the distributor connections. Also inspect the pick-up coil inside the distributor for corrosion as well.
To verify grounds, use an ohm meter and measure from the neg of the battery to the frame and then to a bolt on the plenum. You should have less than 2 ohms. If not check and clean the ground straps. The neg battery cable needs to go directly to the head or block not a bracket. There should be a ground strap from the head to the decklid hinge frame and another from a bolt that holds the trans/engine together going to a spot on the frame on the driver side, The last electrical thing to check is the tach filter. if not grounded properly can cause noise on the signal line causing a random mis-fire.
Hopefully one of the above will fix your problem.
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[This message has been edited by Oreif (edited 12-04-2007).]