Just wanted to give an update. As you guys suggested, I ran into all kinds of problems when I went to install the '70 water pump. How I missed this before sending the pump off to be rebuild, I'll never know, but the '70 pump dumps to the driver's side of the engine, whereas a '69 pump dumps to the passenger's side.
To add to the fun, none of the bolts I bought from AMK for a '69 motor were fitting in the stock locations on the later water pump. I could've fudged around, swapped bolts, and maybe cobbled up something that would've worked, but I didn't really want to. I went to look at the radiator I got with the car, and it looks like a '70 radiator, which means it would have the correct driver's side bottom hose outlet that would've worked with this '70 water pump. That being said, this radiator was WAY too small to have come on my car originally, as it should've had the 24-inch radiator when new, and the radiator I got with the car was much smaller. It almost looked like it came off a 6-cylinder or something, and after looking all over, I couldn't find any part numbers, tags, or any indication that it was an original Ford assembly line part.
So, in essence, once again, the car could've come with a '70 water pump, different bottom radiator hose, and appropriate '70 radiator. It seems strange that someone would've gone through the trouble of finding and retrofitting a '70 Ford water pump to a '69 timing cover, and swapping the radiator and alternator brackets to the later '70 style.
It could've come this way new, but I doubt it, and since I had no way to positively verify it, I bought a '69 water pump and proceeded from there. Everything bolted up as it should, the water pump gasket and bolts fit like they were supposed to, and now I can go with a '69 radiator and hoses without continually worrying about making everything work. From a concours-correct perspective, do you guys think I made the right decision?