Detonation can favor certain cylinders due to engine design making 1 or 2 cylinders to detonate easier that the others. Question is how long did you run the new engine for before you gave it the big boot? Pistons rely on a small carbon film to protect then from the excessive combustion heat. This takes some time to build up.
I agree with wideband sampling all the combined gases. Honda claim to have overcome that problem by referencing the exhaust pulses to the crank angle sensor and adjust individual cylinder mixtures. SO THEY SAY.
I have seen a Delco system sampling at such a fast rate you could see each cylinder fire but which one is anyone's guess.

 

Both times I ran the motor for approximately 500 miles give or take.

On another note I may have a lead on the issue, I have a Dynatek CDI in the car and it did not come with setup instructions. There for I did not adjust the "dip switches". The car ran fine so I figured all was well. After digging around I finally found some setup instructions for the Evo. Dynatek recommends that the switches be set to:
Falling Edge
Restrike or Single Spark
Crank Input

Mine was set at:
Falling Edge
Restrike
Cam Input

A couple of thoughts, being set to restrike maybe it is causing the cylinder to ignite more than once? Second how would it effect the way the CDI operates with it being set to Cam Input instead of the Crank Input.

 

Have you looked at the injector wiring? Just because the injector works doesnt mean its sees a constant signal which means it might be lean (apparently) on that cylinder. The others havent melted which would normally rule out pre ignition but thats the only other thing I have seen that would cause this. Has it just been since the ported head or was that there before and it was okay?

 

I have looked at the injector wiring, all connections look good and I am getting current through to the connectors. I pulled the pins out of the connectors and tightened them so they clip harder on the injector terminal just to be sure.

The ported head has been on the motor for a good while now however it had not been through very many hard pulls as I always had some small issue and had to take it back apart before driving a lot of miles on it. I have however ran this head with out a melted piston issue, I had a ported stock intake and exhaust manifold though.

 

Looking at the pix again closer it looks like the timing is high and likely lean. The intake side of the plug is burnt clean on all of them.

 

is it possible that having the settings on the CDI wrong caused all the commands/readings to be incorrect when tuning causing both tuners to get too aggressive without knowing it?

 

Beings I only have one Evo and nothing to compare it too could someone let me know if this is how the Evo comes from Mitsubishi? This is at the wiring harness to the ECU, I am checking everything due to this failure and it just doesn't seem right that Mitsubishi would wire something like this but I can't be sure. Here are the pictures,
Pin 75 is white then connects to a larger blue wire under the gray electrical tape, this is listed to be O2 Sensor Rear.
Pin 78 is a short white wire that connects to a larger green wire under the gray tape, this is listed as Knock Sensor.
Pin 87 is white and connects to a larger black wire under the gray electrical tape, this one is listed as Avail.
Pin 92 "ground" is spliced in a couple of locations, the wire from the connector goes into the harness and connects to three other small black wires under some black electrical tape, then there are a couple of looped wires that connect to Pin 75 and Pin 87.

 

My evo 8 is the same

 

I think you might have solved it. Cam and Crank are not usually synched the same time. Might be wrong but it's not normally the case so if the cam timing signal is before the crank and the map was assuming it was crank KABANG. Multiple spark will not cause that problem. If the car missed the first time it might generate more heat in the exhaust or burn the exhaust valves but they fire so fast I don't see a problem there.
Another cause of detonation not many people know about is excessive oil burning. Seen that many times on outboard motors when the puddle drain blocks.
I have just pulled my EVO4 down and it's cracked all the top ring lands on the intake side but I know that's detonation. Problem I have now is getting std bore pistons here in Aust.

 

It makes since that the input setting on the CDI could have caused this problem however I would think it would make the car run like crap and it just doesn't make since that two different tuners wouldn't pick up that something was not responding properly. But to this date I have not found anything else that appears to have been installed or not functioning properly. I will continue the search!

 

On the intake side its pre-ignition or lean normally. You would suspect lean would be the exhaust side but it works in reverse. I have never seen a CDI cause a melted piston. Clogged injectors, bad wiring, etc. have done it but not ignition. A top fuel car at 44 amps from each of its 2 magnetos doesnt melt a piston like that on a good run.

 

In the AEM manual, there is a section on setting up a proper noise floor aka knock limit.

 

I agree with John but if the trigger is early by a few degrees it could be the cause. Detonation effect is on the intake side because the exhaust side has rapid burning where the last remaining fuel/air is on the intake side of the plug where detonation can occur. The objective of any engine is to burn all the fuel as fast as possible to eliminate detonation. Lots of people think high octane fuel burns slower but NOT THE CASE it just had additives that reduce the chances of detonation. MSD can only improve burning of the fuel by providing multiple sparks but again if it's too early KABANG. does anyone know the phase angle separation between the cam and crank sensors? I don't think their at the same time. I question the need to have a cam sensor with a race car.

 

I am continuing my testing, trying to find anything that is not right. Last night I sampled the e85 in my tank and it is right at 85%.

Hopefully AEM will be contacting me soon with their results on the EMS test.

 

We switch road race cars to batch fire.