Unfortunately, the 3406E has electronic injectors & computer controlled timing based on all the sensor readings. There's no way to make this engine "simple". Even the throttle system is electronic...the early C-15's are basically 3406E's, as well.Can you take away all of the "other" parts on a cat 3406E and end up with a plain and simple deisel engine?
This is a marine application....The more that can go wrong.....WILL
If you want a "simple" engine, look for a 3406-A or 3406-B with mechanical injection systems. These engines have no internal electronic parts to fail, just a few screw-in sensors for water temp & oil pressure. Good luck with your project!