How to introduce more run into roof?
You've got a flat roof that isn't "true" (straight - you don't want it level).  Your pitch isn't the problem so much as the dips allowing water to pool.

Ideally the best fix here is:


Remove the existing surface material (tar and rubber)    
Remove the existing sheeting    
Shore up the roof structure with extra beams, and shim it as
needed to make it true and consistent from high point to low point.
Install a double layer of sheeting with perfectly flat plywood    
Resurface the roof with ice shield, tar and rubber