Electronic – Why not run high power truck-mounted electronics from the truck’s engine

There are many ways to achieve this. Some are better than others in certain situations, and some only work on certain cars. I'll try to describe a few.

1. This is the most commonly used way. Put a switch (relay, etc.) in line with the starter control signal. This would generally be put before the starter relay itself. It prevents the starter from turning over the engine.
   • Pro: Works on nearly all cars.
   • Con: The car can still be started if you find a way to turn over the engine (pushing the car in gear if it has a manual transmission).
     
     
2. Intercepting a major sensor. These sensors generally deal with crank angle/position. A lot of times a car would only have one, angle or position. They may also be called a cam angle/position. Activated with a switch (relay) intercepting the signal wire coming back from the sensor.
   • Pro: The car will not start no matter what you do since the ECU will think the engine is not turning over and will not provide spark.
   • Con: Only works on cars that use these sensors. Older cars relied on mechanical versions of these.
     
     
3. Intercepting main power like you mentioned. This would require a hefty relay or switch. It is not uncommon for cars to have fuses larger than 100A for the main input.
   • Pro: Would work on most cars.
   • Con: Difficult to do. Easier to find than others (I'm assuming this is to prevent the car from being stolen). Does not work on really old cars that used generators instead of alternators. May mess with modern electronics in the car itself possibly leading to damage.

There are other ways but pretty much all of them would fall under these categories if you want to be able to control it electronically. Don't forget that the car can always just be towed. Once again, I'm assuming you are thinking of theft prevention.

This is really crying out for a switching power supply. The input voltage can vary over a wide range, and is generally quite a bit higher than the 5V out you want. You might be able to find a off the shelf unit that can handle your wide input voltage range. A linear regulator would get quite hot. At 50V DC in, 90% of the power will be dissipated as heat. That's not so much a issue of wasting power, but rather dealing with the heat. For example, if the micro and LEDs draws 100mA at 5V, then 100mA * 45V = 4.5 Watts will be dissipated in a linear regulator. And that's with 50V DC in. 50V AC will produce more than that DC after a full wave bridge, and you say 50V AC isn't even the upper limit anyway.

In addition, something doesn't add up. There must be DC somewhere used to make the spark. Does the unit really not have a battery already? That sounds unusual for a alternator system, although your voltages are in line with a alternator as apposed to a magneto. How is the high voltage for the spark produced?