If the controller is heating up again id also be investigating the pump . Even tho it might seem ok deterioration of the motor can cause high resistance which will make the controller heat up .
As Rossco said defiantly check the connectors at the tank make sure the pins are straight and there are no signs of corrosion. Double check that the controller has a good clean earth as well .
The heat sink does get hot but the unit itself shouldn't overheat If the same problem is rearing its head and replacing the module cleared it up for a few days you are very close to the problem now its a process of elimination . Its good to write down all the parts between the module and the fuel supply and go through them one by one eliminating them from the list could as simple as a crushed wire in the harness between the two or I've come across some one who had screwed something down and the point of the screw was severing the earth wire in the harness but only over bumps etc with the two halves touching most the time Good luck