Hi Pat,
I don't know how old your pedal board is, I'm using a 50+ year old Allen that I looked over closely for wear (felt included) when I added MIDI. I found all the felt to be present and in good shape. But yes, I do have a few keys that do produce their fare share of clicks and clunks as you mention depending on what I'm playing. The lower octave especially does get a lot of use, low G being one of them, and I attribute the noise to how the keys get worn in and return because some constantly get hit by your foot at an angle while others are hit more squarely. The noise you hear may actually be coming from the back of the keys where the key attaches to the spring and as the key gets hit from an angle, returns and realigns itself produces the click you hear.
What to do about it? I've largely ignored the noise so far and attributed it to normal wear and tear. To me the only way to 100% find, isolate and remedy the noise would be to get the pedal board on a work bench and see if you can duplicate the clicks, then by trial and error see if there's anything you can do about it.
I just turn the volume up!
Marc