Has it done this since you got the boat?, it sounds like it's new to you

Not much there besides the shutter wheel and the camshaft position sensor, but worth checking and cleaning the shutter wheel.

I might even try another new cap depending on the quality of the cap you just installed. The Vortec cap is known for misfire issues because of how it's constructed. 

At least you'll have a spare cap if nothing else 

Shade tree test.  Won't hurt anything but might learn something.

Edit update: Fire order on this engine is:  18436572

When you remove the #4 spark plug is it pristine white like brand new or fouled Wet with Gas?

Black from Carbon build up?   The Plug Gap is properly set?   I worked on a Ford 5.4L Truck engine, the owner had it in a shop 4 times because it kept killing Coils.  These are coil on plug engines.  When I inspected it for the source I found a shop put new plugs in it 2 years prior.   After that it needed 4 new Coils, installed one at a time over the 2 year span?  When I removed the spark plugs I found the #8 Spark plug, near impossible to remove in the Ford Truck, I found the previous shop had dinged the plug gap closed when they installed it.  It is very tight and hard to get in there to work but the shop never went back and checked to see why the engine kept reporting miss fires.  They had installed new spark plugs so they never checked them for a possible source of the problem.  With the plugs replaced the coils worked as intended with no more mis fires.  The Ford Computer kept putting that engine into a Limp mode because of the #8 bad plug but the mis fires reported in multiple cylinders not just #8  I have heard when the plug is at zero gap the plug wire voltage can travel through the block and fire other cylinders out of time.

Remove your 4 and 3 spark plug wires.   Take #3 and route it to #4 spark plug.  Leave #4 spark plug wire off for now.  Start the engine and see if #4 is sparking using the #3 wire for a spark source.  It won't make much if any power but it should have a spark you can see all the time.   If this #3 spark source can't make the #4 spark the problem is #4 is grounding the spark plug or the plug is fowled out and dead for some reason.  No spark is jumping the plug gap so your test light can't see it.   The #3 plug is next in the fire order after #4  so a late spark won't cause any problems but might help test and see if #4 could fire with a good known source.

Umm............Somebody needs to tell you that Steve has a Chevy engine

At least your engine runs 

Just so you know you cant time these engines traditionally. what is the distributor off set at?

The only way one can set it is with a diacom setup. if memory serves me,  0 off set plus or minus 2* is the setting..

Could be a cheap and fast solution for this boat.

KENO wrote:   So when does this thing start firing again as you go up in RPM? Does it misfire again on the way down passing through 3000 RPM and then clear up again?

If you dont check the cam offset you are chasing your tail until you know that it is correct or distributor has not moved.

I have seen this before..

and yes you need diacom to check cam off set it.

good luck

I think a good recap of the problem and what's been done is in order here, since however many days and posts later, the word "backfire" just showed up 

Now we have no fire, misfire and backfire all being mentioned.

Your engine should be running at 160 plus degrees, otherwise the computer thinks it's still warming up and your fuel mixture is gonna be rich. The standard thermostat in that is a 160 degree thermostat.

It'll probably run better than is now does with your 140ish temperature, will it fix this mystery firing issue? probably not but you won't lose anything by getting temperature where it should be.

So did you just decide to swap plugs for some reason or did it make the trip to the dealer for a plug swap?

So i guess back at the beginning it really was a great running V7 after all 

You should go out right now and buy 4 lottery tickets in honor of your #4 cylinder.

And......... glad it's fixed

 I changed cap, rotor, coil, cranks sensor, new distributor with cap and rotor,  map sensor, spark plugs, wires,  cylinder heads (one water jacket leaked anyway. Fuel Injectors,  alternator (possible ac ripple to ecm, seemed to get better if unplugged )  Tried another boats ECM,  My next step was to check timing chain backlash and when I pulled the cap it was all burnt up.  So I got a new AC Delco cap and rotor and installed on my original distributor.  All was ok!!! Great,  fast forward  to 5/28/23  Misfire came back exactly the same. Tried Accel cap, no change.  Cam retard is 0.  Ill try an new AC Delco again this week.