If you look on at the outboard side of the engine you will see 3 harnesses and a single wire with a butt connector.
The only connections that are necessary to run the engine are the small triangular connector with a white, blue, and red wire in it. It is outboard of the engine the other connection also outboard is the single wire with a butt connector.
The wiring is rather straight forward in theory. If you look at the B panel wiring diagram you will see the ignition switch with 3 wires on it. The red wire branches off and run numerous things, idiot lights, and instruments. It is connected directly to the Positive terminal on the Starter motor and the battery bank. However just concentrate on the 3 wire harness. When the ignition key is turned on, it energizes the panel through the red wire, when the key is turned further; it energizes the starter motor via the white wire and starts the engine.
The blue wire does nothing as it is an option for an air heater. The blue wire runs all the way to the inboard side of the engine and is taped off even though it does nothing. If you are in there just cut it off at the harness connector on the outboard side of the engine and pull it out and throw it away.
The other wire a single one is connected to the stop button and that is the one that has the butt connector in it at the engine harness.
If you look at my photos carefully, you will see many soldered splices some of which were connected to nothing,
If the engine were grounded, it would be quite simple.
However, it is not.
In addition, Yanmar used plain copper wire instead of tinned copper wire. The harnesses are long and over time, corrosion will eventually cause these wires to lose their full current carrying potential and either short out or just burn up. The USA marine wire is tinned. Just an added thought.
On to the nitty gritty---This where simplicity is thrown out the window.
Let’s start at the heavy black ground wire that runs from the yanmar alternator under the engine to the inboard side of the engine and then on to one of the heavy posts of the valeo solenoid. It is cut, soldered, and taped in numerous places on both sides of the engine. Being that it is hooked to an isolated ground on the alternator all the sensors are connected to it to get the negative battery power to the instruments. Note it is not connected to the block.
The ground from the battery bank is connected to a large post on one side of the Valeo solenoid and ends there, along with the large black wire that runs to the alternator, previously discussed, it is also connected to the negative activating coil contact of the valeo solenoid .
The valeo solenoid is the long tubular one aft of the black Yanmar starter solenoid on the upper inboard side of the engine
The other large post on the valeo solenoid is connected to the block thus, when the valeo solenoid contacts are closed it grounds the block ( connecting the block to the negative side of the battery bank) . The positive post of the activating coil of the valeo solenoid has 2 wires, each with a diode in it. These diodes prevent electric from coming in on one wire and out on the other (which happens to be the stop solenoid). Without the diodes, the engine would try to start and stop at the same time.
Continuing with the starter positive circuit and the white wire from triangular harness connector, Amel spliced, soldered, and taped a heavier red wire near the connector as the harness will not take the load over the distance to the solenoids. I changed this to a 12 gauge wire.
The white (now red) wire then runs under the turbo to one side of the black Yanmar starter solenoid coil (next to the Valeo). Then on to the coil of the Valeo coil solenoid through a diode.
When the key is turned on to, start the engine it energizes one side of the Yanmar solenoid and then the Valeo solenoid through a diode. The Valeo contacts close and then the battery negative is connected to the block, The Yanmar solenoid contacts close, energizes the solenoid on the starter motor solenoid, and starts the engine.
To stop the engine the stop button is pressed and this energizes the stop solenoid mounted in the fuel injector pump. This is powered at the ignition switch. It also closes the Valeo solenoid; again, through diodes to ground the engine. This is the extra wire with the butt connector
As a side note- if the key is turned off at the panel, so is the power to the stop solenoid, you then cannot stop the engine.
That is the theory and if it were to be drawn on paper, it would look rather logical. Unfortunately with multiple connections soldered and taped on important wires all over the place it was a 3 day job to find and remove all these poor connections and add wire to sensors etc. and make for common connection points. If you look at the before photos you will see numerous soldered connections, some doing nothing except extending a wire. I believe a home run on every wire should have been done with this harness, as it is now.
For example, the wire that closes the valeo solenoid coil to start the engine runs from the valeo solenoid, under the engine and is connected to a wire that goes to the Yanmar solenoid. The wire was 2 feet long. I just cut 20 inches off the wire and connected it to the yanmar solenoid 4 inches away through a diode. Of course, many wires that were spliced in multiple places were replaced.
In all fairness to Amel, when the engine is out of the boat and you are wiring this isolated ground on a bench it probably looked pretty simple. However, when the wires are run under, though, and around the engine a lot of wiring no longer makes sense.
Removing the degraded electrical tape and gross spiral Plastic covering is 25 % of the battle. Pulling the wires, out of the covering without breaking anything, is another 20% of the job. Running a new sheath to insulate the engine past the area of the turbo another 15%. The rest is just wiring, heat gunning, crimping, hair pulling, new wires, and connectors.
I hope this makes some sense, I believe I will now rest take a room adjoining the fellow who originally wired this engine in his padded cell in his mental hospital.