In what way did the water/cooling help, did you drive the car afterwards to see if it had cured the misfire ?
It could well be the amp breaking down, but would have expected it a lot sooner, where abouts have you put the amp, maybe it is a area where it is collecting a lot of radiant/transfered heat ?
Does it only play up when hot ?, maybe try another one, a known good one.
tabetha