I'm going to give you quick answers to your questions of the first stones that pop up:

First, what are the best stones to help with study and learning? Hematite, amethyst, quartz w/record keepers, carnelian, orange calcite

Second, what are the best stones for motivation and procrastination? rutilated quartz

concentration? hematite, pyrite
social anxiety and sociability? labradorite, citrine
spiritual attunement? apophyllite
shyness and introversion? smoky quartz
forgiveness? malachite, rose quartz,
creativity? tangerine quartz, ocean jasper
confidence? citrine, yellow calcite, smoky quartz

Is there an optimal color for all the chakras? anything white or clear

Does the size of the stone matter on how strong it affects you? nope

And lastly, if the stone is imperfect does that affect the quality of the power, meditation, etc, or anything? Yes, but does not usually lessen the energy, usually it adds a depth of compassion and empathy.

And do you have any books on crystal healing youd recommend?
http://www.tosots.com/CrystalHealing/bookstore.htm
(I don't sell books, but there is a list here).

This is just a quick reference guide and what came to mind when reading your post. It is not the most comprehensive list, but should get you started. :)