mntlion is a professional -- I'm basically some guy off the street. So listen to him. But I would mold liners first before messing with the shell. Here's what I'd do:
1. Mold the liner. Tons of threads on oven method or water in turkey bag (I prefer oven because it heats both sides, which makes it easier to create space). Read them before trying anything. I'd pull the old footbeds out first. Put your custom footbeds under your foot. Put a toe cap on your toes (and over the footbed), double up on the toecap to get more space. Because you have a good sense of where the boots hurt, cut some foam and tape it to your foot in those where you need more space. Now tape the the footbed to your heel (just one strip of tape is needed, no need to go overboard). Now pull a thick sock over that mess. When the liner comes out of the oven, put your foot in and adjust so it lays flat. Then pull a thick pair of pantyhose (or super thin sock) over the whole thing and slide it into the shell shell. Follow mntlion's instructions re heel lifting and buckling.
Now get back on the elliptical (or whatever) and see how it feels. Continue to determine where the pressure points are and break the liners in a bit more.
2. If that's not enough space, heat mold the shell.
http://blistergearreview.com/gear-re...odacious-boots