Dear Christina,
I'm sorry it has taken so long for me to get back to you.
With the "pedal is optional" marking, I'd put it in as a normal footnote where it appears in print, and show the pedal markings normally.
I'd move the Schnabel-type annotations to numbered references and give them in a special section headed "Editorial Remarks" at the end of each piece. You can say on the TN page that "Editorial remarks are given after each piece."
I hope this helps.
Larry