Learn English – Third conditional would have and would

It's grammatical, therefore would not have been turned shouldn't be replaced with hadn't been turned. The punctuation, though, seems a bit strange.

if...vanquish is an interrogative (question) clause as object of demanded. The clause in turn contains a counterfactual conditional clause had Russia been vanquished and a main clause.

The whole interrogative can be thought of as coming from this original direct question:

The President asked: "If Russia had been vanquished, would the insurrection not have been turned against Prussia?"

Subject-auxiliary inversion for the conditional:

The President asked: "Had Russia been vanquished, would the insurrection not have been turned against Prussia?"

Bringing the conditional after the main clause:

The President asked: "Would the insurrection not have been turned against Prussia had Russia been vanquished?"

Turning into reported speech:

The President asked if/whether the insurrection would not have been turned against Prussia had Russia been vanquished.

Punctuation fix: I would use a period (.) instead of a question mark after vanquished in the reported speech clause. I would remove the single dangling double quote (") before if.

This was written in 1864. I wonder if the punctuation would have been perfectly fine then.

"If you went to bed earlier, you would not be so tired." to me means that someone is consistently going to bed too late and is now (or usually) tired because of it.

I would interpret "If you had gone to bed earlier, you wouldn't be so tired." as more of a one-time occasion where someone stayed up too late and is now tired as a result.

On your second question, "If you had gone to bed earlier, you wouldn't have been so tired" sounds better to me.