I'm refinishing a floor from 1923. The floor was covered with carpet. When removed, there are two large spots from an area rug. The wood is in good condition and I have hand scraped as much gunk as I could off of the floor and sanded with 20 and 36 grit. The wood is bare but the rug marks are still there. Any tricks or tips?

The wood looks like fir pine but the grain is super tight and the wood is like rock hard

The darker areas have been exposed to the atmosphere and have oxidized. The color will gradually disappear as you sand deeper. The wood may never be all the same. I usually stain the lighter color and try to match the existing color that is darker. Sometimes a dark stain over the whole floor will be the most even.
An area rug would be the easiest solution.

The plan is to go with a dark stain. (Minwax jacobean) there really isn't much info on old pine floors out there other then that they are a pain and rare. Should I put a layer of pre stain on?

I have never used pre-stain. After the stain has dried, and the oils have hardened, I use #2 steel wool to firmly buff off any darker areas to make the floor more of an even color. The wood will absorb stain according to how open the grain is. If the direction of the grain is parallel to the surface the stain will not penetrate as well as if the grain is upward or receding in relation to the surface of the wood. Where it has absorbed well you can abrade off some of the stain to make it lighter by polishing.
Many floor guys use stain or pigments in the seal and finish coats to make the floor a more uniform color, with a darker colored finish.