Yes, the digital version will be in PDF format. I can embed the audio after converting it, so it will work fine. When converting from Word the audio will be lost, but I can re-attach it in Adobe Acrobat.
I will be controlling the size of the printed version, so can do some trial runs to make sure the QR will scan correctly. And yes, I'll definitely leave the QR image at a single size for both versions (way too much work to do otherwise).

best, --john