I recently read The Faithful Executioner and it got me interested in the Holy Roman Empire (and German history before the 19th century). Unfortunately, due to the diversity of the empire there don't seem to be a lot of books on that subject (at least on Amazon).=
I am looking for book suggestions on HRE history whether overviews or ones that focus on a particular time period or location.
The best book by far is "Germany and the Holy Roman Empire" by Joachim Whaley, its available in two volumes, or a single abridged version. It starts with the reign of Maximilian I and ends with the dissolution of the empire.
There is also the shorter (but still good) book "The Holy Roman Empire 1495-1806" by Peter H. Wilson.
A couple of tough going academic studies are Benjamin Arnold's German Knighthood and Princes and Territories in Medieval Germany. I'd start with the New Cambridge Medieval History if you can get access to it, though.
There's already been some good suggestions: I'd throw in Thomas Brady's German Histories in the Age of Reformations, 1400-1650, which is Reformation-focused but still gets into the structure of the Holy Roman Empire by extension.
/u/Sid_Burn mentioned Peter Wilson, so I feel obliged to also recommend his magisterial Europe's Tragedy: The Thirty Years War. It's incredibly long, but sharply focused and gives you a great idea of how HRE politics really functioned in the run-up to the war—as well as going over one of the most important periods in HRE, and more broadly German, history.
This economist article cites a few good sources. I've wanted to dig into them but haven't had the time yet (yes i know it's been 2 years)