Are you sure its cylinders 3 & 5 that aren't firing? Have you confirmed that with a timing light? And are you sure you have your wires ordered correctly?
Originally Posted by Stealth316
Ignition Timing The firing order is 1-2-3-4-5-6, with each numerically-successive cylinder reaching top dead center (TDC) 120 crankshaft degrees after the previous one. Paired cylinders have pistons at the same relative position, such as both at TDC, but they are 360º out of phase, such as one is in the exhaust stroke and the other is in the compression stroke. Paired cylinders are 1-4, 2-5, and 3-6. Spark plugs are fired simultaneously in paired cylinders, during the compression stroke for one cylinder and during the exhaust stroke for the other cylinder. The spark during the exhaust stroke is wasted because the basically inert exhaust gas cannot combust.
could not have said it better! if the wiring's correct, make sure that the PTU is okay, as well (diagnostics in the manual). you can actually swap coil locations (swap the primary's wiring on the bottom of the coils) to make sure that the coil itself is fine. If they are, then you're left with either the PTU or the less likely source, the ECU.
Thanks guys, I've had a suspicion it's the ECU but hoping it's not. I'll try swapping the coils to see if it's that (yes, it is definitely 3 and 5, I checked the FAQ in here to make sure I had the right numbers before posting ;-) )
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