Solved the shift problems suggests perhaps the issue may have lied in the ECM?
Well, the "ECU", or some sensor providing input to, or device receiving output from, the ECU.
I'm wondering if OP's 4L80 problem isn't some manifestation of failsafe mode and, if so, what has "failed" to cause it to operate this way.
I might be dreaming but I think I read someplace, recently, that a failsafe mode for the 4L60E (with certain ECU's or certain years perhaps) was to operate in only a few gears. (edit: Is this what happens with a MAF failure on 1996+? Darn, I wish I could remember...)