More specifically, was there ever an independent ruler of Bohemia who was elected Emperor? (Excluding unions such as with Luxembourg and Habsburg rule) As a follow up, who actually did the "electing," was it some sort of council or did the Prince-Elector have any influence or say in the matter?
The Bohemian dynasty that comes to my mind were the Premysls. They never became emperor but were elevated as kings 1085/1198. The electors of the Holy Roman Empire were made up by 7 electors in 1356 where all of it became formalized in the Golden Bull (comparable to laws or statutes or modern day constitutions). You had 3 theocracies Trier, Mainz and Cologne and the 4 sceular rulers the King of Bohemia, the count of Palatinate (later it went over to Bayern), duke of Saxony and the markgrave of Bandenburg (later becoming part of Prussia).