When we pulled the carpet from our bedroom at our last house, we had the same deal with the pad underneath. It must've been installed in the 40's I swear!!!

To remove the gooey mess I had to use a heat gun and putty knife and warm the floor and push the mess off the floor, 1" at a time! Since the room spanned the whole width of the house - it was a 15 X 30 foot room.

I used the same sander as you and had the same issues, the remains would clog the paper, but it gave a nice flat finish. I didn't add stain, just poly over with the first coat cut with thinner. Then "buffing" with steel wool between coats.. oh joy!!