Does it look like the picture I've attached?
If so, then yep, you have a "late, large flange" engine, and the larger flange partially covers the timing hole. My engine was rusted solid in the picture, so I never had to time it....but I have heard others do use the combo as-is and despite the smaller opening, it's still possible to set time that way.
Like 1955CJ-5 said, even if the pump was installed wrong, I think you can still pick the appropriate new cylinder and the marks should work for you.
It'll be tedious, but if you can paint the marks with something that sure would help.
Come to think of it, I was under the impression that when they went with the larger flange in the back, the timing cover got a timing mark, as well as the pulley. So timing could be done with the more conventional method...of course if your engine is a mash-up of parts, previous owners might not have put the later timing cover (with accurate timing marks) onto the engine.
Good luck!