The idea is decent but it could use more work. You could have Reed just invent an eternal time capsule to bury near the rock or anywhere else but that's not really exciting.

Keep the idea of a big reliable marker, but make it something like a particular geological formation with clearly defined stratas from each epoch, due to a lucky quirk in the local environment. Whenever one member of the FF reaches it, they mark the top layer in an unique way : Johnny chars it, Ben cracks it, Reed cobbles a chemical reaction that turns it blue or something, and Sue uses a forcefield to create lines within the stone without cracking it, so it can be felt by touch if you know to look for it.
This would allow each FF to communicate the rough era in which they're to be found, and erosion of the sides wouldn't be an issue.
After that they can just carve the actual coordinates nearby pretty much anywhere provided they go big and deep, because with the stratas already marked whoever get to a time machine first already have an idea of the rough 1000-year period they're supposed to be looking. They can each definitely carve something that will last 1000 years and still be readable.