GT 40 Hesitation

'98 SN with GT40 EFI. Starts a hesitation only after it warms up. Some times the engine needs to be switched off for the heat to soak through. The hesitation is consistent at all RPM above idle. The engine will start and idle every time and responds to WOT as expected with no hesitation observed. There is also nothing observed when run on the trailer, only evident under load. The hesitation is a drop in RPM momentarily of about 100 rpm.

I have done the following:
Replaced correct heat range plugs
Replaced Wires
Replaced Distributor Cap and Rotor
Replaced E-Coil
Replaced High Pressure Pump
Replaced Low Pressure Pump
Replaced Fuel Pump Relay
Replaced ECU Relay
Replaced the two diodes to the ECU relay
Replaced the Fuel Cell Filter and high pressure pump hose
Replaced Raw Water Pump (leaking seal)
Replaced Battery

Conducted Compression test 140 psi all within 10%
Confirmed the Spark timing at 5Deg with SPOUT removed.
Cleaned the anti syphon breaker valve
Cleaned Spark Arrestor
Cleaned all electrical connectors
Cleaned all earthing points
Changed the ECU power source from the battery box to the Assist solenoid.
Checked the function of MAP sensor
Engine Coolant Sensor
Engine Air Temperature Sensor
Throttle Position Sensor
Fuel Injectors have been removed, cleaned, flow tested.
Fuel pressure is 39psi engine running.
Alternator output is 13.5 volts
Power at fuel pumps is 12 volts
A code reader has NO fault codes come up for KOEO or KOER.
The ECU has no obvious defects evident on the board however no ability to test here in Australia to my knowledge.
I have changed the two diodes in the circuit.
Anyone with further suggestions please advise as I am just about at the end with the exception of the ECU which I would have to source from the USA at a fair expense and that may not be the issue. I am also unable to locate a breakout box out here which makes things difficult.
I have not addressed the PIP sensor nor the TFI. Are these candidates for this symptom.
Any Ideas please.

When did it start and what did you last do before the hesitation began? How good are your troubleshooting skills?

With that list of stuff that's been replaced already, why not add the TFI 4 module and the PIP to the list?

People have had PIP issues and replaced a bunch of parts like you did because they didn't want to get into taking the distributor apart to replace it.

Many have replaced the whole distributor instead with a rebuilt one or an aftermarket automotive one with the same part number and reused their marine cap or filled in the vent hole with RTV . The link below is to distributors that people on the site have used.

One with a cast iron gear is what you want The Spectra FD-14 is an example.

link

The module is an easy replacement

A part number would be BWD CBE40 or NAPA TP-29 as a couple of examples that could be cross referenced

Either of these things can cause funky problems like you're experiencing

Then again, you may have something else going on but I;d do these before thinking about replacing the ECM   

Success at last. After some 30 odd hours spent between on water testing and workshop testing the issue has been resolved. Initially found the signal from the ignition module to the ignition coil dropping out intermittently, found there was no heat transfer paste on the ignition module, possibly causing the module to overheat. Replaced the paste and retested with Oscilliscope, massive improvement but not fully resolved. During on water test the hesitation occurred 6 times in one hour. Fault identified as distributor output to ignition module intermittently dropping out. Distributor removed and stripped, found some corrosion and the pickup loose and the Hall effect sensor rubbing on the pickup. New distributor has resolved the issue.

Good job, a lot cheaper than going the ECM route first.

And............you still have a couple months of your Australian summer left