Engine cuts off & will not restart

I have a 1997 Ski Nautique with a PCM Ford engine (GT-40) (about 500 hours on it)that I am having trouble with. Over the last two years, the boat runs great one day and then the next I have trouble. At times, I would be riding or pulling a skier and the boat would just stall and cut off. When I tried to crank it, it would turn over but would not restart. I sometime could wait 30 to a couple of hours and it would restart. Sometimes I could not get it to restart on lake, get towed in and load on trailer, get home hook water up and boat starts fine.

I have had this happen at time when riding/skiing for a while and then have had it happen when I have not been running long at all like less than 5 minutes. I changed the PCC fuel filter and also the small hose on the High Pressure pump inside the FCC. Installed two new relays. Replaced the kill switch since it did go bad about 2 years ago. Spark plugs were replaced about 2 years ago (not many hours on them since I replaced them). Put sea foam and fresh gas in tank. Checked wires/connectors while in yard running to see if boat would cut off while jiggling them around. Alternator was checked last year and appears to be working fine. Think battery is fine. Ignition switch seems to be working fine, all gauges come on when switch is turned on even when boat does not crank.

I am thinking it is something electrical going on as it is not consistent on when the issue happens.

Does anyone have any suggestions.
Will hooking up to a code reader tell me anything?
I have seem someone posted that they had trouble with a TFI Module.
I have also been thinking about the E-coil.
Don't know how to test either one to see if they (TFI or coil) are giving trouble.

Please help as I want to get back on the lake ASAP without any issues.