I can't believe that the mixture adjustment available could correct for a belt being off one tooth.
They are easy enough to move slightly during disassembly- it's possible that you maybe bumped it a tooth as you were removing pulleys? Just a possibility.
I know I've done it reassembling.
The cam gear being off 1 tooth will make a big difference in power and driveability. I don't think it would have been a happy car at all. The intermediate shaft will have only a small effect, as long as the rotor still more or less lines up inside the cap- I think it can take a tooth of misalignment either way without trouble. 740s do not have this as an issue of course.

The other thing i can offer is that it's possible to get the throttle actuator rod out of adjustment during a throttle body service. The operation of the switch can be ok during cleaning on the bench, but then if the cable is too tight or the throttle rod is adjusted too short, it will not allow the switch to close in the idle position (fully closed). Similar to the effects of a REALLY filthy TB keeping the throttle plate open a bit. With it all clean you shouldn't have trouble finding a proper adjustment point.
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Rob Bareiss, New London CT ::: '87 244DL/M47- 229K, 88 744GLE- 218K, 82 245T-181K Also responsible for the care and feeding of: 88 745GLE, 231K, 87 244DL, 239K, 88 245DL, 246K