I had clearly identified that I was not getting a ground from the PCM on either of the two injectors that I could access under the intake manifold. There was B+ on the red lead to each just not the operating ground. That is exactly what PATS does to disable the vehicle in this series. In other applications it can disable the fuel pump and/or the ignition.
After a month of trying to upload a custom tune to the PCM to disable PATS without success I finally tripped to the fact that the Data Port connector was loosing connection during the upload process. The SCT 3015 did not identify a problem, just never completed the upload. Trying to read DTCodes with my reader finally demonstrated the loss of connection.
Bottom line - for the '98 - '01 Explorer a software turn off of PATS is apparently the only solution. While I am sure that a Ford dealer WDS is fully capable of doing that there is not any documentation nor any tech, that I found, that knew how to do it. Ford, obviously, did not intend that anyone in their organization disable their precious PATS. That only leaves a custom tune as a method of doing an engine swap on these engines. To the tuners it is simply a software switch to turn on or off.
Once I finally got the PATS software switch turned off and was getting a pulsing ground from the PCM I was still not getting injector operation. Then I used a straight pin through the wire insulation at an injector to manually apply a hard ground to the PCM side of an injector. I could not detect an operating click by feel or sound. They had to be gummed up from evaporated gas. Professional, out of the car cleaning solved that problem.
. . . and its now ALIVE!