Just a quick summary, I've completed a rebuild on my Impreza motor which is using a Rob tune ECU. In the recent rebuild I've converted my ignition system to COP from wasted spark.
When I went for first start up I wasn't able to get the car to run. It sounded clearly as though the firing was off.
Here is what I've concluded, that either the factory service manual is incorrect in the pin placement at the ECU of the ignition system, or in some case there is different pin placements on different ej20g ECU's.
I originally followed the Subaru FSM which has the ecu pin placement as follows:
Ignition #4 - pin 7 of 26
Ignition #3 - pin 8 of 26
Ignition #2 - pin 9 of 26
Ignition #1 - pin 10 of 26
1996 JDM ej20g ECU pinout picture:

With no luck trying the Subaru FSM pinout and a bit of digging around I found a pinout diagram sent to me by Haltech. I noticed that the Haltech pinout differed from the Subaru pinout, so I gave it a try and sure enough got the car running on all four cylinders.
Haltech pinout as follows:
Ignition #4 - pin 7 of 26
Ignition #3 - pin 9 of 26
Ignition #2 - pin 8 of 26
Ignition #1 - pin 10 of 26
Haltech pinout picture:

Sorry if this old news, but I didn't read anywhere of others facing this issue, unless I'm crazy, maybe, probably.