Excalibur 330 misfire

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.

At least your engine runs 

Could be a cheap and fast solution for this boat.