Hope this helps you out, (Long Story)
My 91 RR 3.9 was having some problems related to a faulty fuel pump relay (this part one is really weird).
I had no power reaching the fuel pump, I traced it to a faulty relay (under the passenger seat) The dummy previous owner had installed one of those home air fresheners driven by the heat provided by a small AA battery, and installed it under the passenger seat. The problem was the freshener vapors were gumming up the relay poles!
While trying to figure out that problem and having the car stranded I decided it was a good time to put a free flow filter I had just bought.
Then when the fuel pump was solved, another problem arise (Part 2).
The engine would start OK cold or hot, would idle very well cold or hot, but whenever the applied throttle was more than some mm of pedal travel it would misfire heavily and could not go more than 20 mph.
After about 2 weeks trying to solve this I found a Morgan Site (has the same engine and EFI) with this info:
http://www.gomog.com/allmorgan/headgaskets.htm#AFM
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Morgan 3.9 Issue with the AFM
The 3.9 Hotwire Injection System has a tricky little issue more commonly found in its Morgan configuration than others.. It can drive the best batty and force the expenditure of huge sums fruitlessly.
It is described in a careful reading of some of the testing procedures found on this site, the Haynes Manual for the car and the Autodata Mechanic Worksheets.
It is absolutely imperative that the AFM (Air Flow Meter) not be grounded (earthed) to the car. Its bracketry will normally prevent this but its situs on a Morgan can easily circumvent this. If the AFM is grounded, it will give aberant readings and the ECU cannot successfully operate the engine.
Morgan places the AFM next to the heater and its hoses on the bulkhead. The hoses used by Morgan and leading to the heater have a high carbon content and, if they touch the meter, they ground it.
Symptoms can range from the car stalling or not starting or racing at 2000 rpm + continually with or without an ineffective throttle.
If you are in doubt, simple test the AFM with your multimeter to check if grounded. If it is, simply change the hoses for higher quality non-conductive hoses or silicone.
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I just had to lift the AFM and put a rag under it, take it for a drive and prove myself those Morgan guys were absolutely right!
When installing the Free Flow filter I left the AFM touching the top shock mount and created this mysterious problem.
Hope this helps you as your symptoms look similar...
J.