Scott, I'd put it back together and run it carefully until you can diagnose where the noise is coming from. It's really hard for anyone to diagnose something you've never heard and some third party is describing from memory. You got some good advice in the 48-60 column.

If it is the fuel pump push rod, it rides on a cam lobe. It could be the cause of a ticking sound, but I wouldn't classify it as knocking.

Also could be piston slap, wrist pin issues, valve sticking and being slapped by the lifter, etc. I've never heard waterpumps make a knocking sound...........

If it's any consolation, my merc flatty has had a ticking sound for the past 20,000 miles. Best of luck with it.