I've done a little more investimigating.
I changed the oil. There were no filings nor debris in the oil.
I tried to get the bike to replicate the knock either by hand turning the wheel or by running it on the center stand and using the brake to simulate a load. I couldn't get it to produce a knock that I could hear or feel.
The sprockets look good to me. On the other hand, the chain has many stiff links (that do not easily move back to straight from curved). I had oiled the chain not long before taking the trip, but my chain oiling leaves something to be desired. I spent all three travel days in the rain, so I'm sure this didn't help the chain.
As for why I wanted to check the master link, it was the only thing, besides the tire, that I had replaced before the trip. I wanted to make sure I hadn't bunged it up.
So, I lubricated the crap out of my chain and then took it for a short ride (it's raining here). I couldn't get the bike to knock, but I'll need a longer go just to make sure. The consistency of the klunk still makes me wonder if it is the chain.
Regardless, I'll order a new chain from Z1 tonight.