I'd pedal once per bass note for the opening and similar sections. The harmonies can blur to a certain degree. With the Cantus Firmus parts, change pedal with the harmony.
I play the Hess transcription, but most of the ones I've seen do require a little bit of organ technique to execute the legato lines. A lot of finger substitutions and crossings. Identify the most important parts: the CF and the main contrapuntal melody. These receive more importance when it comes to maintaining legato than the remaining harmonic lines. If you need to break legato do it with a harmonic part, not a melody part.