I'm incline for the ground issue.

Try to clean, clear, and relive grounds.

Last time I had a weird miss fire, It came to be two cables and 3 plugs melted.

You already did that, so no point looking it again !

Can you enable in you scan program the miss-fires error per cylinder?

Allen Nelson did this on my tune-Scanner, and I was able to pinpoint the problem.

My tune at first had this error disable !