Had the exact same issue when I pulled my boat out of the water two years ago. Went out in late September to pull the boat off the buoy for the season, but was slow to turn over and wouldn't start. Bought the boat two years before and the stickers on the batteries with the dates weren't there, so the batteries were of an unknown age. Bought two new batteries, installed them, boat started up, pulled the boat for the winter until the next season. Next summer, took the boat to the launch, pulled it off the trailer, tried starting it up and just got the same clicking noise that you're hearing. I thought that was really odd as the batteries were brand new from barely 6 months previous. Put the boat back on the trailer, pulled it out and back to our cabin, couldn't figure out what was wrong with the boat. Figured I'd go through and recheck all of my connections going to the battery terminals, etc. Put a wrench on the terminal nut for one of the batteries, was reefing on the thing and managed to barely get it to spin a little bit tighter, and that's all it took for her to start back up again. To be fair, I think the terminals on the batteries are a bit thinner than some of the connectors going to the battery, and I'm assuming they were shifted off to the side and just not making quite enough contact with the terminal. But instead of throwing money and parts at it, I'd definitely start by going through and rechecking all of your connections first as the issue seems to have occurred after reinstalling two new batteries. I'd be willing to bet some serious money that is the culprit, if it isn't though... make sure you don't have a bad brand new battery by testing it, as well as check the battery switch to make sure it isn't corroded and the connections to it are tight as well. But again, if everything worked just fine before swapping out the two old batteries for the new ones and you didn't change up anything else, I'd be willing to bet you've got a loose connection somewhere, or that something isn't making as good of contact as it needs to start up the boat fully. Good luck!
