Hi everyone, I have a new probably with my car and my MS set up

Mazda MX5 NA6 turbo
MSpnp2 MSExtra 3.2.1
Running Toyota COPs, wired into the factory harness. part 90080-02238
I am at the dyno tuning my car and all is well for about 2 hours. I have done my tuning up to 5000rpm and I am now ready for WOT runs. So far no issues. I do a couple of WOT runs, no probs. Next run, I start to get miss fires while the dyno is hold 2000rpm before starting the WOT run. I try again, same result.
I changed my plugs to from NGK iridium to the NGK SE plugs both in heat range 7. I gap the new plugs to 0.6mm. No change, still have miss fires.
I check the dwell and it is 4ms, this is too high for the COPs, should be in the 2.1-2.5 range I believe - this is my fault, I must of re-load the base tune I got and forgot to change it. So now I think, obvious, I have damaged the COPs
I drive home and the issue gradually gets worse.
Following day, I swap all 4 COPs for new ones. I go for drive and the probably still exists.
I have continuity tested my COP wiring, including negative testing all other terminals to ensure that none of the wires are touching others anywhere
Here is the msq and a log, you can see from the rpm that the engine is no pulling cleanly.
https://dl.dropboxusercontent.com/u/107850668/MegaSquirt/2013-11-06_19.24.29.mslhttps://dl.dropboxusercontent.com/u/107850668/MegaSquirt/CurrentTune.msqNote the AFR table might look a bit strange, because my innovate LC-1 is 1.0 AFR different to the reading at the dyno, so I changed it in an attempt to use auto tune, but I abandoned that. Also the VE and spark maps are not 100% finished, but I don't think that is part of the issue?
Any help in diagnosing is greatly appreciated, I have a dyno booked for Saturday and a motorsport event I have entered on sunday.