So i have had a 1986 SN 2001 since 2017 and since then i have been fixing different problems as it sat for years before i rebuilt it.

My latest issue is the boat breaking up under load. After the engine warms up a bit it will start to miss and break up intermittently for a few second and then slowly catch back up and run normal.

It will rev up real quick in neutral with no hesitation. just under load, especially when trying to yank up a skier.

Some background on the latest diagnosis/parts:

Brand new Holley marine carb that runs real smooth. Put an inline fuel filter in as well.

Brand new plugs and wires last year (correct prestolites and wires from nautique parts) 

new coil last year - is producing 12.5 volts to + side when key on

New cap 3 years ago

It has been converted to EI with a breakerless ignition from nautique 3 years ago. It is not being passed through the ballast resistor as i fought with this as nautique says it needs to be used with a resistor but then contacted the manufacturer and they said it couldnt be used with a resistor as it need 12V at all times.

So basically i have replaced all fuel and electric and still am running into issue with misfiring and am all out of ideas.

I read that a faulty tach could cause the issue except i disconnected it from the coil and it still remains an issue

Im starting to think the breakerless igntition is faulty. i thought about replacing or going back to points. I believe the timing is at 10-12 degrees as well

Any information is helpful. Thank you in advance!!

Check the shaft for radial play, and confirm the air gap is not more than spec when you put some pressure on the shaft.

What you really mean to say is that the magnetic ring used in some Pertronix kits isn't used and that your kit is a Pertronix 91581LS or maybe the cheaper 1581LS. 

The 91581LS has a Red magic box and the 1581LS has a Black magic box.

It uses the original rotor and the magic electronic circuitry in the little box senses when a lobe passes by to make a spark that the rotor transfers to the terminals in the cap as it passes each terminal.

Click on the link below, it most likely what you have.

http://www.google.com/search?q=pertronix+91581ls&sca_esv=1de0a4ee025c56b1&sca_upv=1&sxsrf=ADLYWIKPfx6cCAdZWSHNcbVDNZuqnEBdhA%3A1720543176847&ei=yGeNZrCvM_6p5NoP-4Ky-AI&oq=pertronix+91581ls&gs_lp=Egxnd3Mtd2l6LXNlcnAiEXBlcnRyb25peCA5MTU4MWxzKgIIADIEECMYJzIIEAAYgAQYogQyCBAAGIAEGKIEMggQABiABBiiBDIIEAAYgAQYogRI_DBQgA1YgA1wAXgBkAEAmAFmoAFmqgEDMC4xuAEByAEA-AEBmAICoAJxwgIKEAAYsAMY1gQYR5gDAIgGAZAGB5IHAzEuMaAH9AM&sclient=gws-wiz-serp" rel="nofollow - link

The coil puts out lots of volts like 20,000 to 50,000 or so, what you're measuring is the input voltage to the coil from the ignition switch, which is basically battery/alternator voltage. The coil steps it up to the high voltage working in conjunction with the electronic module that grounds and ungrounds the coil as the lobes pass the sensor in the magic box.

Pertronix says to eliminate the ballast resistor just like you did and it works good that way.

Hook up your timing light.  Engine at idle timing might read 11* I think you posted.  Advance the throttle slowly while watching the timing mark.  You should see it advance or move as your RPM's increase.  

Keep increasing RPM while watching the timing marks, it should continue to advance.  Old distributors might continue advancing to 4,000 RPM, newer ones are fully advanced by 3,400 RPM.   You want to know that yours does advance, how much advance it offers.  20* or so is normal, maybe 25*.   Your Total timing would = the setting at idle + the amount your distributor advances.  Ideally you will want the two to add up to 34* approximately.   A set back timing light makes this job very easy if you have one.   IF your timing marks do not go all the way up to see 34* you might need to measure out and add another mark at 34*.  Be careful to measure exactly.   At 34* it will run perfectly, at 38 you might start damaging parts or blowing a head gasket.

If your timing is accurate and smoothly advances each time you have ruled this out.  If it is not moving your distributor is rusted inside and needs to be cleaned up, maybe install new advance springs.

Here's a link to an old thread with some "representative" advance numbers from idle up to full throttle, partway down the first page.

It'll give you an idea what you're looking for.

When you installed the Pertronix kit you would have been looking at the springs and weights at that time.

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=47660&title=distributor-springs-advice" rel="nofollow - link

Umm.........you don't want to buy that distributor in the link for your engine.

You have a Reverse Rotation aka backwards rotating Right Hand Rotation engine in your boat assuming it's original to the boat.

The one in the link is for a Normal Rotation, Left Hand Rotation engine like in a Ford truck with a 351.

You can do a whole lot of reading here on CCF about reverse rotation engines and the difference in cams, cam gears and distributor gears

To tell which way your engine rotates in the marine world, you stand behind the engine, looking at the flywheel and the engine turns Clockwise, it's Reverse Rotation. Or if you want to look from the front, if the pulleys and belts are turning Counter Clockwise, it's a Reverse Rotation engine.

A normal rotation engine is bass ackwards from that 

It can be real confusing the first time you're figuring this out  

Marine distributors pick up moisture in normal use.  The distributor weights can rust and stop working properly or the springs inside rust out and break.   If it does not advance properly you can be down 40% on power.