Try two things and this might help a lot. Try recycling your old foot beds into your new boots. I have a pair of 32 ones I have used in three different pairs. It help a lot. If its that bad toss your old liners into the new shells and ride on. Sounds like break in pains to me, been there so many times, I demolish boots. Heat molding could help since it speeds up the break in time but again it sounds like the normal process of breaking in new boots. Also try different socks, thinner if you need a little room, thicker if you've got room and need a little extra padding, I'm not a big fan of thick socks but it can't hurt either.
When I got my Burton Grails they were great in the store but after about four hours on the hill my heels hurt horrible. Since then they have broken in and are fine now. New boots take about 12 to 24 hours of solid riding to break in. That would about three or four trips depending on how long you ride when you head up each time. Good luck and I hope this helps.