I've never had exactly the same problem you have, but have had sore feet from boots without enough padding under foot, and heel problems from a pair of Merrels that just never quite fit rit. Three things that are worth trying:
1 an insert with a metatarsal support
2 a pair scholls gel inserts for padding
3 a pair of superfeet inserts for the stiffness.
If none of these helps, try a really good shoe store for suggestions or you may need different boots.