What could have gone wrong?

WAY too many variables to guess at but why did you assume the water pump was the source of the leak? Did you actually see it leaking? That could be it but there's a lot of other more likely things to look at first like corroded core plugs, loose hose clamps, and things like that.

Why did you have to replace the generator? They can fail at any time but just removing and reinstalling it won't hurt it. Could some wires have been left off? There might be a really big fuse for it that blew if the output terminal got bumped against the engine and the battery wasn't disconnected first.

Nice catch, but as a former instructor I found it extremely important to use correct terminology to avoid confusion. Along those lines, you actually have an "AC generator". The "alternator" was introduced by Chrysler in 1960 and they copyrighted the term. Everyone will know what you mean when you say "alternator" but the industry has been standardizing terminology and they chose the more confusing AC generator.

That aside, there's no better proof than seeing a leak. As for the altern, ... Ah, ... AC generator, without being there to see how things went down, there really isn't much you can do to damage it. When you can smell it, that's a sign it had a shorted diode. That will reduce the output to exactly one third of its rated current which usually isn't enough to meet the needs of the entire electrical system.

As for the no-start condition, don't disconnect the battery because since the Check Engine light turned on there will be at least one diagnostic fault code stored in the Engine Computer. That code will be the place to start.