1990 Toyota 4 Runner shifting into 4th too soon

I have a 1990 Toyota 4 Runner. It has a problem with upshifting too
soon into 4th gear.
It will shift directly from 1st to 4th or any other combination. It is
intermittent, some days not doing it at all, other days, I can drive
for 10 - 20 miles before it acts up. and yet other times it starts
right out of the driveway mis-shifting.

I bought the truck in August 2005 knowing it had the problem but at a
fairly good price considering its overall good condition. I thought
that it would be an easy to remedy electrical or sensor issue.

However, the first transmission shop insisted on a rebuild of the
tranny. After the rebuild it still had the problem. Further
investigation found some frayed and broken wires. A couple of shops
have looked at it but all they find is more bad wires and they all give
up, although, we believe all the wires are now repaired but it still
has the problem.

I called the previous owner only to find out he "forgot" to mention a
friend of his changed out the tranny for him about a year before in his
personal garage with a used transmisiion (not a rebuild). He also
changed out the ECM computer. One garage suspects a major mismatch as
we have also found transmission wiring colors don't match the computer
wiring harness.

Anyone have any suggestions? One shop mentioned a dealer reflashing
the computer.