In my experience chaps, if the boot is causing that much pain/discomfort, it's either not the right last, or the right size for your foot.
The boots I'm selling were just half a size too small, and caused pain (nothing like blisters though). They just didn't feel comfortable on my foot.
The boon dockers I'm wearing now, in the correct size, were just comfortable from day 1.
The right last, the right boot, you won't even feel like you're breaking them in hardly.