Gaps that wide are impossible to fill. Are you sure about the width of the gaps?
Fillers will limit the movement and obviously, there has been movement there.
Wide pine being a softer wood, may have absorbed the stains deeply. You wil have to considerable sanding to get them back to clean. Spot sanding will always be obvious..
Have you considered taking them up and having them reinstalled?
A proper installation will take care of the gaps and will break up the scratch and stain patterns. You may lose one room due to new cuts and throw aways, but one room could be done with new wood and would look great.
It sounds like the flooring was not cured before installation. New flooring needs to set in a home and dry before installation, giving it time to shrink and settle into the climate you intend to keep in the home.
Would love to see pictures, What is the pine floor installed over?
Welcome to the forum, I wish I could give you a quick fix idea.