Is it possible (and how do I do it) to change what word Auto-Correct chooses when I make a typo?
You can use the text replacement feature OS X has. To get to it, open System Preferences and choose the Keyboard settings. Head over to the Text section and add as many typo corrections as you please. For your particular examples, you would click the + and put "wil" in replace and "will" in with; "rhoughts" and "thoughts".