I've already ordered a Joe Gagan pot to put in.
See how it goes. Intermittent behaviours are really tough. You only really know you solved it if you see the fault. Changing stuff out you have to play the wait and see game over a long period.
The surprising thing is moving that pot wire had a large effect. Didn't it stop the clipping issue as well as the crackling? So either that helped but didn't solve the issue, or, you are seeing random behaviour and touching anything in the general area is changing the behaviour (for good or bad).
A common fault with pots is the rivets on the terminals don't have solid connections between terminals and track. With something like a wah pedal, where there are mechanical vibrations, the pedal movements could any promote bad contacts to crackle.
Hopefully the new pot works out.
If it doesn't you should try anotherjims cap on the base of Q2 to ground (say 22pF to 47pF). Mount the cap close to Q2. I'd also leave the pot ground wire connected to the ground side of the Q2's emitter resistor.
My guess is that by moving the wire from lug one i applied some pressure to the wafer and the made the wiper temporarily to make better contact with the carbon track. but the problem wasnt only the wafer.
I did the following to be sure the pot is bad. used a wooden clothespin to apply some pressure to the wafer. that eliminated the most of the problem, but the pot shaft is loose as well.
Turning the pot with hand didnt bring up the crackling, but when i started, at the same time, to turn and move the shaft a bit off center it started again. New pot had the same loose shaft so i didnt bother to solder it.
Thats why i decided to order a new, better quality, pot.
Every other component is triple checked to be within specs, voltages looks ok, i maintain a wariness about the inductor but after what anotherjim suggested to do it seems to be ok
The trick with moving the wire eliminate completely the clipping issue,
As soon as i get the new pot i will install it play a couple of days ( or a couple of minutes...depends

) and see how it goes.
Thaks again for the info
BR
Harris