I just stripped my red oak hardwood floors and there appears to be poly burned into the wood. Not staining is not an option because when the stain was sanded off it revealed lots of discoloration. What stain should I proceed with. My thoughts are gel stain or penitrating stain with lots of dry time and then wipe with mineral spirits. Am I on the right track. After the stain am I better off with oil or water based poly to avoid blurring and other problems. If I use gel stain do you water pop before hand? Can the gel stained be thinned a little because the grain of this floor is amazing so I do want it to show through.

Poly-urethane does soak into the grain, below the surface. It can be hard to sand off all the finish. Sand more of the finish off the surface. Once you are to bare wood the stain can soak in and have a uniform appearance, hi-lighting the grain pattern. First grade red oak will have mineral streaks, burls and small knots, along with both heartwood and light sapwood. Staining this grade can make it more like select grade as the color becomes more uniform. The mineral streaks will blend in better when you stain a light brown. I use a walnut color and thin it down with neutral with a 2:1 ratio, I sometimes use 6:1 for a color that comes close to a "varnished" floor from the Thirties.
If you would like a more saturated color, water pop the floor after the final sanding. You will get a darker color and usually have less visible scratches from the sanding machines. Water-based poly-urethane is very clear, so you will see the grain a lot better and there will not be the yellowing from oils in the finish, that will amber. Better workmanship is required for a very clear finish. A dark color will protect the color of the floor better than a light colored stain. The wood will amber, too, but the darker colors will mitigate this type of yellowing as the stain will block the light penetrating into the wood.
Be sure to make a sample on the floor, or better yet, while you are choosing the color, apply the stain to a loose piece of wood. You will not need to re-sand the sample patch off the floor. A water-popped floor may show more of the texture of the wood on the surface and not be as smooth as without water-popping. If you pop the surface, be sure to let it dry thoroughly before staining.