Battery charger "Incomplete" issue

[smiles33]

I bought a used electric Yamaha cart a couple years ago. It's driven about 1 mile/day 3/week. It occasionally has the red "Incomplete" light show up on the Yamaha charger, so I bought a 50 watt 48 volt battery maintainer. It's worked fine in the past.

A few days ago, I saw the Incomplete light so I went to plug that maintainer in using alligator clips directly to the terminals (one on the red terminal on the first battery and one on the black terminal on the last battery connected to the cart, per the maintainer's directions). It didn't work at all (no lights, no charging), so I bought a new maintainer.

Directions said to plug the maintainer into the wall first, which I did. Then I connected the red clip and when I went to connect the black clip, it sparked. I freaked out and immediately moved the clip off.

This has never happened before. I'm not sure if I have a problem with the maintainer or the golf cart batteries. The batteries were brand new 2 years ago, but I'll admit I didn't realize I had to regularly refill it with distilled water. I didn't pay enough attention to the orientation when they delivered it. Anyhow, when I popped up the covers, I could see the tops of the plates about a year ago (one year into ownership). I refilled each battery with distilled water, used the maintainer, and it was fine. I was good about refilling water every 2 months or so but then forgot this past summer. I could see the tops of the plates again so I refilled with water once I saw the Incomplete light.

Did I completely screw up the batteries? Do I need to scrub the terminals with baking soda and water? Do I need to call the local Yamaha shop and have them send someone out? Or could it be I just got 2 bad maintainers?

Thanks in advance for helping me out.