03 Super Air, no start issue

[Jeffwaldo13]

I have a 03 Super Air Nautique 210 Team edition. Unfortunately I did not get to use the boat so much last year. I am pulling it out after a 10 month slumber. First off, and I know I will not here the end of this but I left my batteries connected the entire time. Not sure what I was thinking but it happened. The batteries were brand new last year so I put them on a trickle over night, put them to a load test and they were good. Here is a list of my events so far and hopefully you can steer me in the right direction.
1) hooked up batteries, turned switch to "on", flipped toggle switch, put in code, and press "start" 2 times. All gauges flicker and light up like normal. Press "start" again and I get nothing.
2) I noticed one of the battery switches was cracked and had a tiny arc when switching it back and forth, so I bypassed switch wiring battery directly to engine. Same results.
3) Removed starter and had it tested. Tested fine.
4) installed starter and connected my remote starter to the solenoid, powered on boat using keypad and was able to get it to crank over multiple times with remote.
5) Attempted to start using keypad again, still no cranking but I did hear a faint clicking sound.
6) I got a second set of hands at the helm pressing the start button and was able to locate the clicking. It's was one of the 3 relays on top of the engine.
7) I swapped through all of the 3 relays only to find the same "no crank" result on each one.
8 ) visually checked all the breakers under steering wheel and everything seems good.
9) not sure if this a reliable diagnosis for the "natural safty" but.......when I put the throttle into gear I no longer hear the clicking from the relay, same in reverse.

Now I am unsure as to what would be my next step. I have a nice multimeter for any voltage test and I am not afraid to "Dig deep", just need some direction from this point. Please let me know if you have any questions.

[core-rider]

Bypass the kill switch just to make sure that isn't the issue. Also the toggle switch near it for "All On", "Bilge Only" to make sure. Those switches have issues with going bad as well.

With your multi meter make sure you're getting a good 12VDC signal to the starter relay. I'd also check voltage while trying to crank. If there is a large voltage drop that would indicate possible bad batteries or poor connection between them and the starter.

Does the fuel pump cycle when you first try to start?

[Jeffwaldo13]

I put both batteries on a load test and they checked out fine. Both of them also crank the engine over with the remote start. Just curious, does this not indicate good batteries? Will check voltage if You think it could tell me something different. Kill switch and toggle switch are functioning properly. I can't recall as far as the fuel pump cycling. I will check as soon as I get home. I appreciate the input.

[Jeffwaldo13]

Update:

1) With my volt meter I have tested the three way toggle switch as well as the kill switch. They all tested good and are functioning properly.
2) I attempted to start motor again to find same "no crank" results.
3) I'd also like to add, When I am powering on, the fuel pump is not cycling.

I am truly stumped here. Boat interior is completely dismantled at this point, so I'm in it to win it, just tell me what next. Thank you.

[Jeffwaldo13]

I tested for power to gateway box and it is reading 12v although I am getting nothing coming out to the ECU. Is this normal?

[core-rider]

Sorry, forgot about it turning over with the remote start.

This may be a longshot, but worth checking. In 2003 Nautique had a few wire harnesses where the pins for the fuel pump relays didn't make good contact and worked intermittently. I find it hard to believe your boat has made it 20 years without this issue as mine showed issues within the first few weeks of ownership. I removed the relay from the socket and bent the spring clips out so they would make better contact with the pins on the relay. I haven't had an issue ever since. I did this to all 3 relays at the top of the engine.

Also check the terminals at you gateway to make sure they are tight. The nuts backed off on mine causing electrical issues until I snugged them up.

Maybe check power at the "Start" circuit breaker? I would suggest checking power on both sides of the breakers in the first wiring diagram below.

Here are the wiring diagrams in case you don't have them.

https://www.planetnautique.com/CorrectCraftManuals/GT40EngineManagementHarness.pdf

https://www.planetnautique.com/CorrectCraftManuals/GT40EngineManagementHarness.pdf

https://www.planetnautique.com/CorrectCraftManuals/WiringDiagrams/40PINPLUG2003.pdf

[core-rider]

I would suggest checking for power on both sides of the 15 and 12.5 amp circuit breakers.

Those links don't seem to work... trying again.

https://www.planetnautique.com/Corre...entHarness.pdf

https://www.planetnautique.com/Corre...INPLUG2003.pdf

https://www.planetnautique.com/Corre...WERHARNESS.pdf

[Jeffwaldo13]

I have checked all 3 ofthe relays for power. I have even swapped them all around with each other. Still getting nothing from any of them. I have also opened the breaker panel under the steering wheel tested and even replaced the breaker for good measure.

[core-rider]

I have checked all 3 ofthe relays for power. I have even swapped them all around with each other. Still getting nothing from any of them.

If the pins in the relay socket aren't making good contact with the relay itself then it doesn't matter how much swapping you do. Like I said it's not likely the issue, but worth checking.

[TBrick7]

Do you have a fuse inline from the battery to the helm? I had a model year 2001 and this fuse went bad on the lake and could not find the problem till after a tow in and then trouble shooting it in the garage. With the arching of the switch that might be a problem. It could be blowing that fuse before it gets to the battery.

[NautiqueTim]

Have you checked the neutral safety switch on the transmission? The cable may need adjusting.