So, if a Cleric has an item that gives him a +4 to Wisdom, or a Wizard has an item that gives him a +6 to Intelligence, are those considered temporary bonuses when determining bonus spells and skills?
For the first 24 hours, the bonuses are temporary. After that, if the bonuses persist, they are considered permanent as long as the effects persist. See the headband of vast intelligence item description for an example.
Note: The skills given by the Headband of Vast Intelligence are spelled out in the item description, you don't get more on top of those listed. Just for the record.