You just might be onto something here...
I know the instructions say to run water through to minimize any off flavour given off from the pads in the first little bit of filtering...the concept of using citric acid might not be a bad idea! We use citric acid at work as a first step in doing a quick clean of our RO membranes (350 gal/minute RO system)
I might play around with that and see what happens. I have a turbidimeter here and I could measure the turbidity of the unfiltered citric acid (mixed with distilled water)...then the turbidity of the acid after filtering for 30 seconds, 60 seconds, 90 seconds and 120 seconds....that would give a pretty good indication of how much (if any) fibers, color, etc it is removing. I'd also be interested to see if the turbidity goes up...how long and how much is required before it comes back down again. That would indicate how long it would need to be filtered for until it gets to it's clearest point.
Edit: I also have a colorimeter...I'll run the samples through the colorimeter as well. The colorimeter (as the name implies) may give a better indication of any color being stripped from the filters.