Replace stock Harmonic Balancer?

The previous owner swapped out the pump and timing cover for the one with the marks on the driver side. I guess I don't follow with finding the zero mark. Once I find TDC will the 0 mark on my timing cover point to 0 on the dampener? Or are you saying it might point to a different number on the dampener and then I use that as zero from that point forward?
Good that you know all of that. If things are perfect on all parts, then the 0 on the new damper will line up on the 0 on the timing cover marks. If they are off a bit, then the 0 on the damper will line up on some other timing cover mark. Use that other mark as your new reference, and read the timing tape numbers on the new damper against that new reference point.

BTW, I can't emphasize enough to use a tool like a dial indicator to find exact TDC; eyeballing it is iffy at best. This is the baseline for everything else so it needs to be spot on. 3-4 degrees off on cam timing will show right up in the engine's performance.