The head cooling mod will help with the coolent flow issue, but does nothing to help the piston to wall clearance. After romping through the gears, the car will get heat soaked. Hitting 5th gear at WOT puts an excessive load on the engine. This extra load causes heat, which cause pistons to expand... you do the math.
The revised heads with the coolent flow issue didn't come out untill Jan 05. No Cobra came from the factory with them. Some of the late run 04's did have 9 spark plug threads. That is the only difference.
It's your car so run it how you want, but I would stay away from WOT past 4th
