The cossie ignition system is very sensitive to noise on the ignition trigger lines, mainly attributable to less than perfect earthing arrangements, which gets aggravated with age. The second connection to pin3 is essentially a ground reference for the trigger circuit running directly from the ECU. In theory (from memory) I believe it may well run without that connection, but I'm not surprised you get misfire problems as a result, noise on pin3 produces this problem.
You can connect pin3 of the amplifier to ground directly, while you are at it make pin2 as good a ground as you can make it too, this as standard goes back through the loom to connect to ground remotely which is less than ideal.