Thanks for the replies and apologies for the slow response.
I finally got physically more able to sort the issue out and actually got out on it for the first time yesterday.
Having tested and removed all other possible issues I sent the ECU off for testing and it was stuffed,
A word to the wise is to ask the dumb questions when dealing with repairers, ask them what they are actually replacing it with?
Happy that the bike is going but disappointed it now has no immobiliser (US model ECU)
I fitted a replacement and did a 50K trip Freeway and around town, running fine. Hopefully stays that way.
As I read here "It's a Turkey shoot" dealing with the faults that occurred and tracing them.
Having a dealership not doing their job right in the first place. Replacing a ECU without verifying what took it out in the first place.
Then doing a piss poor effort of repair on said component.
The coils were then replaced.
They failed to diagnose a faulty plug cap and had fitted a incorrect plug to that cylinder. (so they new something wasn't right just couldn't diagnose it)
Intake sensor was not connected correctly.
And finally the ECU who's price has now doubled for a 07 fazer.
Great to know the electronics on this bike, and anyone going down this same path, spend the day exposing all parts, download the electrical section and work your way through it thoroughly.
Thanks all and safe riding