The imperial title as it was could not be transferred from one emperor to a noble who defeated him. The non-Brandenburg electors would not accept this clear violation of their privilege and neither would any other HRR prince beyond the closest Brandenburg-Prussian cronies like Anhalt or Dortmund.
The best one could do within the framework of the imperial consititution (partially unwritten and spread ovber a lot of documents) woulde be the forced resignation of the Habsburg emperor plus the guarantee that not Habsburg would stand in the next elections. But even then it is far from sure the the Hohenzollern candidate would get more then two votes - I assume here that beating Austria involved either an Prussian alliance with Saxony or the Prussian occupation of Saxony and the ability to dictate terms to the Saxon elector.
That still means a shortage of five votes (Bavaria, Palatinate, Cologne, Mayence, Treves), most or all of them catholic, who would likely not vote for an protestante emperor. Electoral Brunswick (ie Hanover) might vote for Prussia, or not. It's difficult to force an elector who is King of Great Britain.
If by some fluke the 1803 reorganization stands, the situation is highly different.
You have Baden (prot), Bavaria (rc), Bohemia (rc), Brandenburg (prot), Hanover (prot), Hesse-Kassel (prot), Regensburg (rc), Salzburg (rc), Saxony (rc), Württemberg (prot). IOW, five protestants, five catholics, with the difference less important than before.
Now, the election of a Prussian king as HRE might happen anyway, but after a strong defeat auf Austria, a peace treaty forcing the Habsburg emperor to abdicate and to guarantee the votes of Bohemia and Salzburg for Prussia would probably do the trick formally.