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Repair 2000 Yamaha 40 hp after years of no use

lakeboat1

New member
I'm looking for advice on how to repair/rebuild my outboard motor. I have a 2000 Yamaha 40HP, 4 stroke (the model is F40TLR) that sits on a small pontoon boat (16 ft) on a lake.

Some back story into this outboard: It was maintained by my dad who was an excellent mechanic, but unfortunately no longer here. The boat ran for a few years after his death, although it had some issues. A few years after, it started having a lot more issues, including needing the impeller replaced since the motor wasn't "peeing." The last few times it was taken out, the motor would turn over and would take a long time to catch including multiple tries, putting it into neutral forward to raise the RPMs, replacing the starter, and carb start spray. Sometimes if it did catch, it would stall while in neutral so you would have to throw it into neutral then throw it into forward to keep it from stalling. Honestly, the motor has always (in the 15 years I have used it) had a hard time starting up, however, these last few times were much worse.

I was able to get the lower unit almost removed, minus one nut holding the shaft onto the upper unit. I ran out of time and someone was hired to remove the lower unit and replace the impeller. The guy who was hired broke something and kept the lower unit for a few months "trying" to fix it. Once we got it back, unfixed, we took it to a mechanic to repair whatever he broke (I can't remember what it was) but I hadn't had the time to replace it.

For 2 years, I haven't had the time to research and repair the motor so it sat on the back of the boat sans lower unit and in the full trim up position. Now I have help to maneuver heavy parts and brainstorm, so I'm looking to finally repair the motor and completely redo the entire pontoon boat (stripping it down to the floats and rebuilding everything including electrical, but keeping the same motor). Of note, the trailer for the pontoon is long gone, so the engine was removed while the boat was still in the water and will need to be put back on in the water (we have stairs on our seawall that ensures the engine stays above the water while we can still attach it). We are also repairing the pontoon in the water which adds a different element. The motor is attached to a stand and I have the entire helm/console sitting near it, but will need to connect it to test everything before reattaching to the boat.

I know I should replace the oil, oil filter, fuel filter, spark plugs, and timing belt. Is there anything else to repair? Since I have the lower unit taken off, I might as well replace the anodes. Should I redo the impeller/cooling system kit (including the gaskets) since it was replaced 2 years ago but hasn't been used? The motor really isn't in bad shape, everything is still clean and there is no rusting, but I'm willing to replace things now instead of down the road. I have heard that this isn't a great motor and I'm sure it's not the best, but I am looking to get better at repairing and would rather attempt to repair it myself so that I can get more confidence and knowledge under my belt and hopefully buy something more reliable down the road. Additionally, I have other engines that need repairing but this is a higher priority so hopefully I'll learn some basics to help me with those. Please give me advice on anything else I might need to consider, I'm sure there is plenty of questions I don't even know to ask! I appreciate any information you can spare :)
 
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