Can a foot metarsal stress fracture hurt more first thing after waking up and feel fine after walking around for a while?

Typically no: You should get an X-ray to see if there is a fracture or other bone abnormality that may be contributing to your pain

Not typical.: You symptoms are not typical for stress fracture, but some directed imaging could help isolate the problem. i'm thinking more of a soft tissue cause. More of a detailed history would help with the diagnosis.