Can my crown on my lower molar be causing my upper molar to fracture and a lot of pain and headaches?

Unfortunately, this sounds very realistic. If the bite is incorrect this can cause unwanted pressure being placed on that tooth and the opposing tooth on top. This unwanted pressure can directly result in pain on the tooth. Sometimes, a dentist can remove some of the porcelain to correct the bite but it sounds like in this case that too much of the porcelain would have to removed to correct the issue. In this case a new crown is very possibly needed. Good luck!

If the crown is hitting hard
against your upper tooth, this can definitely be the cause of the sore top
tooth. Teeth do move with time depending on your bite and periodically
crowns, or even natural teeth, do need to be adjusted to eliminate the teeth
hitting too hard against each other. Many dentists use
porcelain-fused-to-metal crowns, and if adjusted too aggressively, the metal
can be exposed and can be unsightly and rough. Your dentist may be able
to adjust a little bit on the lower crown and a little bit on the upper tooth
to eliminate the metal being exposed. If this is not an option, you may have to
have the lower crown replaced to obtain a better bite and also better
appearance. If you do get it replaced, be sure to ask your dentist about using
a metal-free. All-ceramic crown as an option instead of one supported by
metal.