Hey mate,
I had the same issue with my cruiser for quite a while. After being told it was a common problem by the fuel injection guys and encouraged to part with $3,500 for the exchange pump, I decided on a lot of google time and found the ecu and the pump use a speed signal input.
The light-bulb moment for me was when I dropped the trans into neutral when moving and the engine would still rev on when removing throttle. Come to a complete stop, and the engine would rev and drop normally. That was the moment I realised it had to be the speed signal input to the pump commanding fuel to be injected.
I pulled the speed sensor plug (down on the trans) and presto, she drives like a dream. Fuel consumption is down too I think (at least it feels as though it is). The engine did stall when rolling up to a junction, so you need to wind on just a little throttle using the manual throttle advance (luckily the HDJ is still manual in that department). Idle up at about 750 which is no biggie. Seems not to have affected the AC advance so no problems there.
The down side now is I lost the speedo and the aftermarket cruise (it uses the same speed input signal). I'm on here now looking for a pin configuration for the instrument cluster as I am hoping to reconnect the trans sensor, have the speed signal come into the cluster and operate the speedo and cruise as normal, but then cut the output signal to the ECU so that the pump is not receiving the speed signal.
If anyone knows of the location on line for HDJ79 (1HD-FTE) wiring diagrams I'd appreciate it.
Give it a go mate, such a better drive!
Cheers, Stu