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I have 164 LS engine which I'm setting up for GoTech MFI Pro.

It is running Mode 4 - standard Bosch 60-2 missing tooth with what I believe is a Pajero coil pack (wasted spark) with cylinders 3 & 4, 2 & 6 and 1 & 5 Siamesed together. The issue is that only one of the coil packs (cylinders 1 and 5 black/white wire connected to pin 3) emits sparks, there is no spark produced by the other 2 coil packs. There is only one green light which flashes during cranking - I guess there are supposed to be two?

On the face of it, it looks like the ECU is sending out all the ignition pulses to ignition output one, even though the Mode is configured to 4.

Any ideas?

So the folks at Gotech think that the air gap is too large between the toothed ring and the crank position sensor. It is actually 0.8mm. Only one of the green lights on the ECU flashes when the engine cranks - apparently a sign that the CPS is faulty since when all is well, both flash.
Looking at the CPS, this seems reasonable as it is mangled:
The current CPS is:
BOSCH PN= 0261210