How can I remove scratches in polyurethane?
The best answer I can give you without seeing the piece is to slowly start sanding away the finish over the scratch marks until they fade away. Visible scratches are always much deeper than you want them to be, so they're probably going to require removing some material. I'd recommend the sanding block so you remove it in a uniform manner. You don't want it looking like there is a dip in your table. 

If you do need to re-apply the stain, it's going to be very difficult to match the color. Put on as little as possible and wipe it into the wood with a paper towel, removing the excess. Let it dry, the first time it should be lighter than what you have. You can slowly shade it darker and darker till it matches again.

Then reapply the poly.

Sorry, probably not the answer you wanted to hear with the table being so close to looking done. But if you want the piece to be beautiful for a lifetime, it's worth taking the extra week now to finish it out nicely.