How about setting up a rabbeting bit to cut 1/4" (maybe 3/16" would be enough if the correct bearing could be found) and use it to cut a relief across the bottom of the shelves. You would need some type of support to set in between the shelves to support the router at the edge of the shelf, and probably a stop at each end to control the width of the cut. That would give you 1/2" depth of cut after a couple or more passes. At that point, you could see if the bit could be hung further out of the collet and take more passes - or switch over to a top-bearing pattern bit (most 1/4" shank bits seem to have 1" cutting length although that might be too long) and use the recess already cut by the rabbeting bit to guide the bit until you get to the depth needed. One thing to take into account - you say that the shelves are attached by nails through the sides, need to be careful on the width of the recess to make sure that the bit doesn't hit a nail. As previously recommended, some sincere groveling may be the best approach.