I have answered your querstion on the Aquamist forum, now retored to working order.
http://www.aquamist.co.uk/phpBB2/index.php
copy of my answer...
It appeared the red and green wire on the FIA2 is reversed. When triggered, the FIA2 starts turning on the fuekl injector, flooding the engine and caused the misfire.
For the time being, wire the red wire to a known 12V (steady) and put the green wire to each leg of the fuel injector until a flasjng green led is establish. You can then reconnect the red wire back to the correct leg of the fuel injector.
One question, It there resistor pack in series with the fuel injector?
Richard
PS it would be better to post it to the Aquamist specific section when you have a problem, I visit there everyday.