I follow your advice PSIG and went over the injector circuits connection by connection. I was unable to find any issues so I went ahead and washed the PCB in the dishwasher. After it was all cleaned up I put it on the boat and was able to power up the Speeduino without the injector 3 mosfet heating up.
While everything seemed to be working well, I did notice the injectors clicking after the engine finished cranking. Each time I finish cranking I could hear about 4 injector clicks in quick succession.
I cranked over the engine a few times without anything interesting happening. Then I got my wife to crank the motor over and move the throttle while I sprayed some 'Start Ya Bastard' into the throttle body. Pretty quickly she came to life, if only momentarily. I didn't get a chance to experiment with the settings as my computer had run out of charger and the charger was left at work.
I'm guessing the main issue now is getting the fuel / air mixture right so I can get a working base tune. At the moment I'm working with the attached tune. Where is the best place to start when trying to get a decent base tune?
After reassembly, plug in the mega and power it vis USB. Measure the voltages on the gate of each mosfet. If they are different (and the resistances measured were the same before the mega was installed), it indicates a problem with the mega itself.
Thanks Apollard, I will go back and do this in the morning and see what comes up just to be sure.