Hi Jimbo,
I’m not being funny either when I say you don’t make it any easier yourself. It takes a while to search the meagre snippets of info in your various posts and use Google to decypher the munged up part numbers and manufacturer names. It’s a good exercise in detective work,though! 
All the jargon would be in your speed control instructions,complete with diagrams which you could have got by email from Astec.
To put it in layman’s terms would take ages.OK but you did ask for it :-
I’ll try predicting your answers if only to duck the cranks on the forum. I see two varieties on this thread.
Bear in mind everything below is conjecture based on what you might answer to questions.
So you have got a 12 battery? Y/N
If YES then what powers the acoms receiver? Do you have 4 pencells? Y/N
If NO your speed control is supplying it with 5 voltsthrough the red on the 3-wire connector. If so, that is the root of the problem.To do that (work your boat with one battery) you have a 5 volt supply via an LM2940 or LM340 or 7805 to supply the receiver,servo and all the electronics and relay coils within the speed control.
That device has a thermal cutout that will operate at 150 celcius and so it is placed on an aluminium heatsink. Without the heatsink it can only self-dissipate 2 watts and supply 250mA (1/4 amp) when its input voltage is 13 volts.(2x six volt lead acids)
Your acoms receiver is probably a 20 year old one drawing 110mA ,add the rudder servo and those relays that give the clicking noise and you have in excess of 500mA. That 500mA comes from a 13 volt battery…..OK so far?
That 500mA causes the 5 volt supply component to draw 6.5 watts,supply 2.5 watts and burn off 4 watts.
That’s why the piece of aluminium is scalding hot and needs ventilation.
1. Supply that five volts from a receiver battery and disable the battery elimination circuit (bec) and you can then use a sealed box. OR
2. Reduce b.e.c. heat loss by cutting your drive battery so it is nearer to 5 volts
That 4 watts is what sent your drive transistor over its temperature limit to destruction because it needs a heatsink for large motor currents too,not a 4 watt heat source bolted to it.
What knowledge does yor repair guy have? Did he see any sign of a thermistor to prevent that happening? – probably not.
What you have is a piece of equipment that is poorly equipped for the folk who use it. I note from this both you and Penny Lee have witnessed the unfortunate "malfunction" behaviour of these units that auto store there setting and loose it when there is a power supply disturbance.
Who else has noticed this?
Tom
After typing that I have no enthusiasm to for the long version on your battery charger Lee wants in that link.