So I thought I was a pretty good programmer until I ran into a bunch of different classes I did’t know about. How many class’s are there in total? And if there are a lot which one’s do you think are the most beneficial to know.
Classes?
Classes?
Thousands and thousands and thousands.
Then you can go make some more 
If you are talking about the U3D API - look at the Script Reference.
For .Net classes look at MSDN.
You can even make your own classes lol
Do not even bother to read through reference. Start programming right away. If you run into any problems, google for a solution or post them here. You only need to learn what you need.
on the left side in runtime classes are all classes of the unity api listed. count them yourself. but what does it serve you to know how much they are? you only use those which provide the functionality you need. and from them only a few methods/elements. same for .net/mono. so dont bother about what is there in total and extract what you need from unity. i would estimate i have never touched 70 to 80 % of the unity classes as they are rather exotic for me (android stuff etc).
that you can only answer yourself as noone knows what you want/need to do.
worst advice ever dude, the reference saves lives!!!
so if you run into trouble go through the reference! if you can solve it, google it! if you can’t find it ask here!