I think you can consider many ways during the adventures to give either inherent or permanent enhancement bonuses. If it was up to me however I would try to make them rewards related to the story, and probably I wouldn't let the player choose all the time.
Kobold Avenger said:
-For one thing would it better to have to change the inherent bonuses given out by such things into enhancement bonuses?
Definitely ok in my opinion. You can also make tomes more interesting IMHO if you consider the following changes:
- allow SOME books to give enhancement bonuses (so that they don't stack with boost spells): you don't need to make ALL of them enh bonuses, those with inherent bonuses can still be around on their own
- consider the option of making those enh-type books bonuses STACK; you're going to control the availability of these books in the world, so it doesn't matter to you exactly what rule they follow, as long as the result is what you want; making them stack allows you to let character finds more books later without having to say that the further books are necessarily more powerful (they could simply contain different knowledge)
- consider the option of having these special tomes affect more characters, without "vanishing" after the first read: this will result in everybody trying to read the tome but it will also make characters increase secondary stats (Str for Wiz, Cha for Ftr...) which is more interesting than always bumping the primary stat. Still keep the limit that each character can only use the item once.
BUT
- make is so that a roll is required to gain the enhancement bonus, so that even if everyone will try the item, not everyone will get the benefit (you could make it so that the DC is increased by your current enh bonus in the stat, so that further increases are more difficult)
- finally, CHANGE THE IMAGE OF THE ITEM

it doesn't have to be a book to be read, it could be a fountain to drink from, it could be a test to pass, a prayer to recite in a special place, or even something to eat.
Kobold Avenger said:
-Let the stat boosting spells be affected by permanancy (still not decided on what the costs should be).
It's an option, but to decrease the need for stat-boosting items you could also use the 3.0 versions of the spells, or at least their duration.
Permanency could be better because it frees up the spell slots completely, until a Dispel Magic breaks it.
Kobold Avenger said:
-Rituals/Invocations (from Unearthed Arcana) with some sort of conditional terms for having the stats boosted. More spontaneous ones would be blessings I guess.
This could work as the tomes above. But also it's nice the idea of having conditions and/or expirations for the effect. For instance the party paladin might get a special bless as long as he's fully devoted to the current mission.
Kobold Avenger said:
-Magical locations, going on a quest to a certain place boosts a stat, and does so relatively permanant instead of a year like many magical locations