Hi kojab its a gen 2 and that makes sense about a wet plug being a short and not firing. Which could quite possibly be what's happening, it only does run on one cylinder atm, can feel which ones are not firing by touching the exhaust manifold. Number 2 runner is red hot and the others are cold...
  
I will test your method with the timing light and see what happens...if you go back a couple of posts you will see I posted some pics of the coil to dizzy lead...the end was chewed off, looks to me like it was arcing out in the coil socket which could possibly create a weak spark...I dunno I'm just having a stab in the dark...
 
Next step is remove plugs clean and dry
them, unplug injectors replace plugs and turn over a few times.... that should hopefully clear the chambers of any unburnt fuel...
 
EDIT: now it won't even fire on one which is leading me to believe my coil is dying/dead, tried testing the spark against a bolt on the engine and it is a very very weak spark, only just firing one off....even the leads aren't putting out much of a spark and the spark it does fire is erratic and small ....I will test with a multimeter as per the bgb tomorrow and confirm...

Ok ill throw a new set in tomorrow and see what happens...
Cpu part number is 89661-17321
Located at Phillip island Vic.
I have a megasquirt pnp sitting here, but want to get my car running right on the stock cpu before I install it.

I have what seems to be the exact same issue, I installed my Megasquirt today and it still has the same problem.
 
 

I realized that the o2 sensor must be ****ed as the ecu was never getting any signal from it at all, I plugged the aftermarket one into the Megasquirt and it helped slightly the AFR would start at 14-15:1 then drop to 10:1 after 10 seconds or so.
 
Took the coil out and had a look and the connector to the dizzy was all corroded but resistance was still in spec. I've cleaned it up and put it back in, then tried to ground a spark plug to the intake manifold to see the spark and now the car will not start at all....I can hear the starter solenoid engage but the starter does not move, fuses all good have to troubleshoot it more tomorrow.
 

No no thanks for letting me drive your car it was brilliant!
 
On my car I think it was the corrosion on the coil, after i fixed that up its now running at 12-13:1 at idle which is still very rich but I think it must just be the base tune on the mega squirt that needs adjusting.
 
It's hesitating when I slam my foot to 100% throttle too the afr will drop to about 9:1 for a moment then jumps back to around 11, running fine otherwise though. I am assuming it just needs a tune...though if it sounds like something else was happening let me know please!

As above, I just replaced coil, igniter, O2 sensor and banged a new set of plugs in. Runs as normal. Idles at 14.7 goes 10 when I boot it,

asimovy, im still yet to hook up my mspnp, so I dare say yours is just the tune.