Jon, where are you located? I sold Hewescrafts for a while, very familiar with them.
Ive seen simuliar problems before and 9 times out of 10 this problem is caused by a bad ignition switch. Although that helm is fairly well enclosed on those boats and failed ign switches are usually caused by being exposed to the elements. Does i happen every time you go out? I keep a spare wiring harness with a key panel plugged into it laying around the shop that i use either when problems like this occur or when working on larger boats so i dont have to climb in and out the boat so much. If i were working on it, i would hook the auxillary wiring harness and switch to the motor and see if i can get it to fail to narrow it down to a boat or engine problem. Its probably going to be a boat side problem, those Hewescrafts are great boats but the utility of them sometimes overshadows the attention to detail and i did occationally have problems with sharp edges wearing and breaking wires.
Has your dealer replaced the side mount control box? If he really cant figure it out and pinpont the cause thats probably the first step i would take.