The E4OD gets signals from the FIPL (or TPS) Fuel Injection Pump Lever, the tach sensor and the rear anti lock brake (RABS) / speed sensor on the rear diff housing. Check the FIPL first.
The TP (FIPL) sensor is incorporated to provide an electrical signal, which is proportional to the amount of fuel being delivered, as an input to the Transmission Electronic Control Assembly (TECA) Based on this information, the TP (FIPL) provides the proper shift scheduling and torque capacity.
Should a malfunction occur in the TP (FIPL) sensor circuit, the electrical signal sent to the TECA will be recognized as erroneous. When this out-of-specification signal is detected, the TECA will provide a high-capacity operating mode that protects the transmission from potential damage. This operating mode includes maximum TV pressure, resulting in harsh upshifts and engagements and a singular shift schedule regardless of accelerator pedal position, resulting in the 1-2, 2-3 and 3-4 shifts occurring at a speed commensurate with a heavy (but not wide open) throttle setting.
The Ford shop manual has a procedure to set the FIPL sensor. It's fairly long and required a special gauge block and the use of the Super Star Tester (early scan tool). I decided that this was not what the "field" needed so I called the Ford Hotline and they gave me plain and simple voltage readings at closed throttle and WOT. MUCH easier.
Closed throttle voltage = 1.1V
WOT min 0f 3.8V not to exceed 4.3V
You definitely don't want 5V at WOT. PCM would read this as a short between Reference Voltage (5V) and FIPL signal and go into failure mode.
Next, does your tach work? Bounce? If it does not work, or bounces, then replace it.
The dead tach sender should/would send the automatic trans into a "failure management mode" (limp mode) with harsh engagements and firm shift feel, and an abnormal shift schedule. It has no effect on a manual trans only the Tach readings.
Replace the tach sender on the oil fill housing a big 1" nut with 2 wires. Ford only part Engine RPM sensor E5TZ-17B384-A about $50. You can remove and clean it but usually changed later too. You can test it too, hold it in the air away from ferrous metal, using an ohm meter lead on each wire you need DC resistance between 2000-3000 ohms.
Does your speedo bounce? If so replace the sensor on the rear diff.
If all of this "passes" then check all of the electrical connections at the tranny it self. Remember to replace the heat sheild on the pass side of the tranny when checking the connector.
Now, after all of this is done, replaced and good, remove both negative batt cables for about 15 minutes, this will reset the computer.
If you have not already done so, invest in some nice plate style coolers (I run two), a temp gauge and go to the local dealer and get a trans pan, gasket and filter for the 2001 F250 4X4 with a 4R100 trans. This will give you an extra 1 1/2 qts of capacity and a drain plug. Magna Fine makes a nice disposable in line filter, or you can add an external filter of choice.