References for learning about acid and bases in organic chemistry
Concerning your first question: I found that the  book "Organic Chemistry" by Clayden, Warren, Wothers and Greeves and here especially the 8th chapter contains a very good and readable introduction to acidity and basicity. After you have worked through this chapter you should be able to explain why certain molecules are as basic/acidic as they are and you see a lot of typical $\mathrm{p}K_{\mathrm{a}}$ values for a lot of substance classes so that you get some knowledge about what $\mathrm{p}K_{\mathrm{a}}$ values you can expect for other substances. As for your second question: If you want to know why reactions occur in the way they do you'll have to take courses in Organic Chemistry. Apart from that, I wholeheartedly recommend the aforementioned book again. If you work through this book (this will take you a while: it has 1200 pages... but then again, that is 1200 very readable pages :)) you'll have a very solid basis in organic reaction mechanisms and organic chemistry in general. If you want to dig a little deeper this book by Bruckner is very thorough but a little dry.

One particular perspective that I found very helpful in explaining why reactions happen in the way they do was the frontier orbital theory. A very good and readable book about its use in organic chemistry is this one by Fleming. The book by Clayden et al. also uses this theory a lot in explaining reaction mechanisms.