Thanks for your reply. I've used the same reasoning as you, ending up with a dual amp setup as the ideal for my needs. But I felt I needed some confirmation before spending a lot of money on two new heads (the JCM2000 has two series loops btw).  

A follow up question, would another unit (for example the Eclipse) give a better end result? I guess the rack units have more processing power and better converters than the Pitch Factor? Or would it be overkill to use such a unit as a dedicated harmonizer in front of two amps?