shift position is most likely due to revving the engine in N.
the pulser coil may or may not be related to the charging issue.
the battery code is due to the ECU saw a voltage below about 10.5.
your voltmeter should show above 13V even at idle.
were a lot of issues with the regulators on that motor if the cables failed or were loose or corroded.

The shop replaced the rectifier last year. Is that the "regulator?"

yes, some manuals refer to it as a rectifier,some a regulator others as a regulator/rectifier.
its a throw back to the days when the regulator was a separate part of the rectified and regulated charging systems.

are you sure the pulser coils were not unplugged while the engine was running while someone was testing??????
it happens.

record then clear the codes.

I bought the boat with 156 hrs. 3 months later I took it to a Yamaha shop because the rpms would max out around 4200 and when you trim the motor it would try to stall. They replaced the rectifier, changed filters, and cleaned injectors. The voltage seemed like 13-14 volts according to the gauge but towards the end of the season it seemed like it was on 12volts running or not, and she cranked slowly forcing me to switch to two batteries at times.

Since then its been sitting and I am taking advantage of winter to get it ready. I can turn a wrench but am new to Yamaha outboards which is why I purchased the cable/software. The only way the pulser would have been disconnected is if the shop who did the work did it.

Maybe the pulser is the cause of the low voltage since the rectifier is less than a year old. Its logical to me but I understand the regulators are sensitive. I'll have to mess with the software and figure out how to clear the codes.

Thanks for the help.

The trim causing the motor to stall and the slow to crank would lead me to believe that you have a power supply issue.

Is the battery in good condition? Are the battery cables themselves and their connection points at both ends in good condition? If you have a battery switch is it is good condition? Are the fuses and fuse holders in good condition (clean, tight and free of corrosion)? Are all ground connections clean and tight?

Measure the battery voltage as close as you can to the rectifier/regulator. See diagram below. Should be approximately the same as the battery voltage when that voltage is measured directly at the battery. Hopefully, it is more or less 12.7 volts. Start the motor. The voltage should rise to more or less 13.5 ~ 14.5 volts after a brief period of time.

By the way, it is the lighting coil that provides AC voltage to the rectifier/regulator. Not the pulser coil. If the R/R is not outputting proper voltage then check the lighting coil output.

Any questions, holler.

goes back to a digital voltmeter and a voltage drop test on the cables.
the reason for the stalling when trying to use the trim was a loss of voltage to keep the ign system,the fuel pump the injectors and the ECM powered up.

that engine needs about 9 amps just to remain running.
toss in a sudden load like trim, an additional 25 amps or so, and if the battery/cables are NOT top notch. stalling will occur.

***-what a great bunch of info! By far the best no b.s. forum I've come across! I'm about to go mess with it. It used to stall when trimming until the shop did their work. Before I took it in I cleaned all grounds and connectors on the battery cables and the posts themselves. I replaced the wing nuts with regular nuts and tightened with a wrench. I also trickled charged the batteries and it still cut off. It does not stall anymore since the shop did its thing.

To clarify, the pulser does not contribute to the charging system? What does it do? Tells the ecm when to spark? Timing? Just curious why I could have gotten that code.

I am getting about 12.62v at the batteries and the engine. When it first started it climbed to 13v at the engine and steadied between 12.5-12.65. So it looks like I definatly have an issue. I tested on a ground wire and a big red wire where the fuses are that leads to the starter. I unplugged the rectifire to gain access to the AC voltage in and it reads between 18.5 - 19vAC. Hopefully I did not hurt anything by unplugging the rectifier. The ignition was off. Is that good AC voltage?

Stupid question - can I disconnect the negative cable from the battery and see if the engine stalls like an older car with charging issues? Or will something get damaged?

Low voltage to a motor can cause stuff that is dependent upon voltage to act up is all sorts of ways.

The pulser coil has nothing to do with the generation of electricity relative to charging a battery or supply voltage to operate electrical components on the motor.

Maybe more than you wanted to know but here goes:

Pulser Coil
(Crank Position Sensor)
The ECU receives a signal from the pulser coil to determine position of the crank, and engine speed, for proper ignition and injector timing by “reading” marks on the outside of the flywheel.

Lighting Coil
The lighting coil construction is usually bright exposed copper wire with a lacquer-type coating wound around an iron core. Lighting coils for 2-stroke engines are independent coils located under the flywheel on engines through 70hp. On engines over 70hp and all 4-stroke engines, they are built in with the ignition charge coils. If the charge coil or lighting coil fails, the whole stator assembly must be replaced.
When the flywheel magnet passes the coil, a current is generated inside the coil. The amount of current generated is dependent on the strength of
the magnets, their distance from the coils, the speed of the flywheel, the number windings in the coil and the number of coils. The single phase charging systems usually have one lighting coil and a flywheel with two, three or six magnets. This represents 4 pole, 6 pole or 12
pole charging systems.
Most electric start, two-stroke engines through 70 hp have 6 pole systems with an average output of approximately 6 amps. The 75 hp through 90 hp
2-stroke engines incorporate a single phase 12 pole charging system with an average output of 10 amps. The three phase charging systems have a stator with three lighting coils and a six magnet, 12 pole flywheel. All 115 hp and larger 2-stroke engines and 50 hp and larger 4-stroke engines incorporate this three phase system.Output varies from 10 amps on the 50 hp, 4-stroke engine to 50 amps on the 300 hp HPDI 2-stroke engine.

DO NOT confuse a CPS with a pulser coil.
the F115 US market uses two pulser coils and another magnet on the rotor to CORRECTLY spark.
lose a coil and its all good the system simply defaults.
the F115 does not use a separate CPS.

DO NOT use a generic manual or the inter webb to COMPARE sasquatch to bigfoot.

When I'm on my **** I always start with the cheap stuff and prefer replace over clean when the value of my time rivals cost. The big wires on the battery provide starting power, the little ones do the rest and grounds are common.

I near sent a gps back until I found a corroded inline fuse that passed enough juice to run for five minutes before dropping voltage too low for the unit but still lit the gauge lights. Due to regular "cooking", a buddy kept prerigged starting harnesses until he figured out a ground strap went bad.

Before replacing yamaha parts, I suggest replacing the wires. In saltwater environments corrosion can travel under the Insulation. Our boat was rigged with water proof crimp connectors by the original dealer, but they didn't heat shrink the covers. Be sure to use marine grade and not hardware store spool, otherwise you'll enjoy a bad rerun. For a few bucks, you'll know that's not the issue.

Good luck and keep us posted.

Do not do this to you motor or even automobiles anymore.
It can damage the charging system along with other things

thanks. I am going to get the batteries tested just to make sure they are still good and replace the rectifier. It will still be a while before I get on the water since winter here in NC is abnormally cold his year... really upsetting to the global warming folks! I will post an update when I get it done in case someone else out there has the same issues. thanks again - you all have helped a lot.

Update: I replaced a battery and changed the rectifier/regulator.I cleared the old codes and she is now putting out a solid 14.35v while running and a pleasant 12.9 with key on engine off. I have not had it in the water yet this season but is great on muffs. Just thought I'd give an update for anyone coming across this in the future. Thanks for everyone's help.