You could test for spark when it fails to start.

Do you have to give it  some throttle when you're restarting it when hot?

You had issues about a year ago that a float adjustment took care of, now you may have to do some "twiddling", AKA tweaking, on the idle mixture screws to get it to start better after it's hot..

See the link below for some info that might help

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=48605&title=hot-and-cold-starting-89-sn" rel="nofollow - link

I recommend that you do NOT use starting fluid...particularly on a warm engine.  Bad engine ju-ju.

You can verify if the coil is producing a spark.  Lisle makes specialty tools and such for the automotive industry and makes a decent, low-cost spark tester that is easy to use:

JQ

Based on your last post you may need to clean your idle air bleeds (and the main air bleeds while you're at it.)

There are pictures in the link below of the air bleed locations on a Holley.  

The outboard holes are the main air bleeds and the inboard holes are the idle air bleeds.

You might as well do all 8 of them with spray carburetor cleaner and compressed air. (4 on the primary side, 4 on the secondary side, all shown in the picture). It can also be done with the carburetor apart blowing in the other direction, internally to external, but this is easy and usually works.

Like the writeup says, you can do it in place, then I'd set the idle mixture screws out about 1 1/2 turns as a starting point and do the previously mentioned "twiddling" to be sure you're idling on the idle circuit.

If no luck, you'll have to take the front bowl and the metering block off and make sure all those tiny passages associated with the idle system and it's air bleeds in the metering block and carburetor body are clean and blown out.

Having rebuilt it last year, I don't know if you might have blown out the air bleeds or not. Lots of people never go near them

Somebody is bound to jump in and say that isn't a marine Holley 4160, but that OK, the pictures are only to show where the air bleeds are located. 

As far as the guys thoughts on ethanol, everybody has thoughts, not all the same.

You could have other issues but this is a cheap easy start.

You're right.........it shouldn't run at idle speed, but 1000 rpm isn't exactly a good, normal idle speed either 

So you need to back up a couple of posts and do the cleaning mentioned.

At 1000 rpm in gear, you're drawing most of your gas from the transition slots and not the idle circuit, so closing the idle mixture screws makes no difference.

So if you clean things like the air bleeds, then with the idle mixture screws about 1 1/2 turns out as a starting point try setting your idle down to 650 to 700 or so in neutral and tweak for a smooth idle adjusting both the mixture screws and speed screw as necessary to maintain the low idle speed..

When that's good, you can put it in gear in the water and the idle should drop maybe 50 to 100 rpms and idle smoothly. You can then tweak on the mixture screws for the best smoothness and see how it responds.

Like mentioned before, you could have other issues, but try this first before the other stuff gets discussed

Can you make it idle at that 650 to 700 rpm speed right now or is 1000 as low as you can get it to "idle"

At a normal idle speed with fuel being supplied by the idle circuit you should be able to look down the throats and see no gas because all the gas is going into the engine under the throttle plates which are barely open.

Try it just the way it is and see how it responds when you put it in gear, you might have to open up the idle mixture screws slightly or it may be just fine

No, they didn't use a ballast bypass during cranking on your engine. 

The voltage readings you are getting are very low. What are you getting at the battery? Then a reading at the ignition switch, then at the balleast resistor and finally at the coil. You should have 8 to 9 volts at the coil. Report back to what you find. 

Adam,

How are you checking volts at the coil? Disconnect the negative wire and check again. Also, as mentioned,  check for a drop at the ignition switch. 

I don't think you've said that you have points under the distributor cap, but assuming that you do, the 10 volts at the resistor input side and 5 at the coil (+) is not a bad reading if the points are closed when you check the voltage.

If the points were open you'd have the same number at the coil (+) and the resistor input since the coil is doing no work.. In your case 10 volts at both.

If you unhook the negative wire at the coil(and the gray tach wire too for good measure, like Pete mentioned, then check the voltage on the coil (+), it should be about the same 10 volts at both spots since the coil is doing no work.

The 10 may be a little low and that's why he said to check the voltage at the key switch terminals (and check the connections tight too).

Then you could unplug the 8 plug connector at the back of the engine and check all the plugs clean from corrosion or clean them up to be sure you're not losing some power there.

And.........PCM didn't use a bypass like mentioned, but it would be easy to wire and give you the best possible voltage to the coil when starting the boat. 

You would run a wire from the "I" terminal on your start relay/solenoid to the coil (+) terminal and when the key is in START, you get full voltage with a short direct path going to the coil. 

After the engine starts and the key is now in the RUN position, the "I" terminal has no power supplied from the solenoid so it supplies no power to the coil, but the coil is getting power from the normal path from the keyswitch to the ballast resistor to the coil and with the alternator now running you have more voltage to the resistor and the coil.

Click on the link below for some talk about this jumper (affectionately known as the Zach Jumper ).

It just automatically does what you did with your manual jumper.

You can call it a band aid or whatever for a voltage issue in your wiring but it's easy and as you showed with your temporary jumper, it makes your engine start

There's really no down side to doing it, you could find and cure your voltage issue. and decide to leave the jumper installed.

And if you happen to have an electronic module hiding under the cap, all this stuff still pertains.

If you want a drawing for installing this jumper, just say so and one will magically appear tomorrow 

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=47003&title=no-start-no-luck" rel="nofollow - link

This is a mid 80's diagram courtesy of TRB, which may be a little newer than yours but you have a solenoid and a coil just the same, so adding a wire as the blue squiggly line shows would accomplish the "Zach Bypass"  12 gauge is a good wire size for this