I do not like the mechanics as written. Knowledge checks, especially knowledge checks made when on an adventure, reprsent the knowledge the characters have 'on hand'. Just reading a book once should not provide a permanent benefit, unless the books are magical, such as a Tome of Understanding or the like.
Instead of gaining a permanent bonus after reading each book, how about letting the characters amass a personal library that grants a circumstance bonus to either knowledge (any one), spellcraft or decipher script checks equal to the square root of (cost spent / 250)?
i.e. Cost of library = bonus squared x 250 gp
We use 250 gp because circumstance bonuses are better than competence bonuses -- comparable to the difference between luck bonuses (2500 gp) and enhancement bonuses (1000 gp). If the character wants bonuses to more than one skill, she can buy a seperate 'library' for each skill.
It should be reasonable that, for all the many benefits of broad reading, you generally do not memorize each and every book you read. Therefore, it should be reasonable to need to have the book at hand[/b] to gain the benefits. Also, one single book seldom containes the width of knowledge that one skill point represents -- Knowledge (physics), for example, will cover quantum mechanics, classical mechanics, classical electrodynamics, fluid dynamics, high energy physics, astrophysics, etc. etc. -- it is better to say that the bonuses come from a collection of many books relating to similar topics.
If you really want the characters to be able to get a permanent boost, I suggest using a Tome-like mechanism -- ie. a magic book that grants inherent bonuses to a skill. Let each wish spell grant +2 inherent bonus instead, up to a maximum of +10 inherent bonu, so the books would grant +2, +4, +6, +8, +10 inherent bonus to a single skill.
Spellcraft for Dummies: This delightfully illustrated handbook contains formulas and theories on metaphysics and the nature of magic, but entwined within the words is a powerful magical effect. If anyone reads this book, which takes a total of 48 hours over a minimum of six days, she gains an inherent bonus of from +1 to +10 (depending on the type of tome) to any spellcraft check she makes. Once the book is read, the magic disappears from the pages and it becomes a normal book.
Strong evocation (if miracle is used); CL 17th; Craft Wondrous Item, miracle or wish; Price 27,500 gp (+2), 55,000 gp (+4), 82,500 gp (+6), 110,000 gp (+8), 137,500 gp (+10); Cost 1,250 gp + 5,100 XP (+2), 2,500 gp + 10,200 XP (+4), 3,750 gp + 15,300 XP (+6), 5,000 gp + 20,400 XP (+8), 6,250 gp + 25,500 XP (+10); Weight 5 lb.