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To isolate the problem I jumpered the start lock relay in the trunk so that it didn't need the signal from the alarm box to allow cranking. Once I did this i could crank the car every time, but it wouldn't always start. This showed me that the starter and ignition switch were fine.
This led me to the alarm box, as if the ecu does not get the correct signal on the W line, it wont allow the injectors to fire and if the start lock relay is not jumpered, it wont allow the car to crank.
So then I hooked my oscilloscope up to the W line to see what was happening - when the car would fire right up, the signal was being sent straight away, and I could hear a relay click in the alarm box when it did so. When it did not fire up, no signal on the W-line and no click.
I checked the signal from the key decoder to the alarm box, and that signal was being sent every time, so I made the assumption that something was wrong in the alarm box. I opened it up and checked the signal to the clicking relay - it got a signal every time, but didn't always switch over. swapped it out, and it was good to go again.
If you are not comfortable with electric and electronic fault finding, I recommend just buying and ECU, Key pill and Alarm box matched set from Woody and swapping them out. Its a pretty simple job to swap them.
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