Evan, I personally have found, that a deep rich stain is hard to achieve when a wood conditioner has been applied. I have found that the wood conditioner does a good job in uniform stain, but seems to act as a block or sheild on prohibiting the stain from soaking in deeper. Since the conditioner has been applied, you would have to do some re sanding to remove it if even possible.
Secondly, I hope that the stain your using does not have poly mixed in it already. Again I have found that a deeper stain effect is hard to achieve when the poly is mixed into the stain, It also acts as a shield and makes darker richer staining hard to achieve.
Don't know if either situations pertain to your project.
My favorite stain for oak, red oak, is Golden Honey Stain, but it is not a deep rich stain and hard to really darken much more than the second pass. But darker stains may get you what your looking for.