I'd put 2 coats of POR-15 silver under there, you brush it on since spraying it is dangerous and requires breathing apparatus due to the isocyanates.
The silver has a lot of aluminum ground up in it to help fill and smooth out the low pitted areas on a rusty surface. This stuff is tough and dries hard, almost like powdercating.
Just wire brush off the loose rust and follow the directions, I think you'll be pretty happy with the results.
http://www.por15.com/