Depending on the gauge of metal a stud puller likely won't move it anyway.  They are great for small dents in door skins, quarters, fenders and other light gauge metal, but on the heavier stuff they tend to just snap off without moving the metal.  Your plan is the best method.  You can also shrink the metal if needed by heating it up with a torch and letting it cool.  Don't quench it as some people recommend.  It will shrink enough from just cooling in the air.  Quenching it tends to embrittle the steel making it harder and more likely to crack.  If its really pushed out of shape you'll need to shrink it because the metal will have stretched.  I used this method to fix the lower radiator support in my '89 GT. 

I've picked up a set of sub-frame connectors from Street or Track as I'm going to be using their 3 bar rear suspension and they include the mounting point for the longer, lower control arms already installed.
I figured I'd open the floor, hammer things flat then weld in a nice hunk of steel in the bottom of the frame rail so that when the car gets lifted there again, it won't deform.