Everything you mentioned could cause the rather unspecific pain you mention.
Another possibility:
https://ice.riedellskates.com/products/boots/255-motion says it has a "Plus our higher box toe and forefoot relief area". If that means the foot bends more near the ball of the foot, it might be more than your foot can comfortably and safely bend there.
It is also possible the place where it bends does not match the location of the ball of your foot.
If the heat mold isn't enough, you can start playing with making your own insole, or with modifying the current one's shape with tape or adhesive foam (like moleskin, molefoam).
If you are in a hurry, and can find a really good skate technician, they might be able to help. So can some PTs, podiatrists, and some orthopedic surgeons who specialize in feet, though they don't come cheap.
But it helps a lot if you can "listen to" your body - e.g., figure out exactly where it hurts. Is there more or less pressure on the boot there? Does it take a while after you start skating for it to occur, so it might be rubbing (as in starting to form a blister), or one part of the current insole might be a little higher than the corresponding part of your foot, forcing you to use extra muscle to control the boot?
A lot of people have to experiment a bit to figure out what eliminates their particular pain. But it is well worth it - not only is it good for your feet to eliminate problems, but pain can be very distracting, and misfits can affect skating performance in other ways.