Do the bonus skill points from Ioun stone Scarlet and blue sphere stack with Bonus skill points from Headband of vast int?
I know the bonus +2 int won't but what about the skill?
No.
The skill points is a consequence of getting a permanent bonus to int. I would argue that since you do not get the bonus from the other item (due to them not stacking), you do not get the skill bonus.
Mechanically having the headbands grant ranks in a specific skill, is an elegant alternative to getting retrospective skill points to distribute, which are lost once the item is removed.
In my personal games, I rule that whichever item has the greater CL is the one that has effect over the other.
In the FAQ you find:
"If I wear a headband of vast intelligence, do I get retroactive skill ranks for my Int increase in addition to the skill ranks associated with the item?
No. The skill associated with the magic item represents the "retroactive" skill ranks you'd get from the item increasing your Intelligence. You don't get the item's built-in skill ranks and another set to assign however you want."
The enhancement bonuses overlap, they do not stack.
The skill points are derived from the intelligence bonus, so they do not stack.
Essentially you could wear both at the same time and designate which one is "active" to get the appropriate skill (and language, if you play it that way) immediately. But then the other is switched off.
Otherwise your skill ranks total wouldn't match your intended total (by intelligence and class skills) anymore.