I'd get it set right and leave it (fit the standard values). With all those variables you will either, just confuse yourself and spend forever endlessly twiddling knobs in search of a sound you will never get, or you will end up with a favourite setting and leave them there. Referring to the title of your post - Difficulty with dialling in a tone - with so many variables on trimmers, all of which adjust over a wide range, some of which is not useful since you would never want any of them adjusted down to zero or even much less than half, it is not surprising you cannot settle on settings you like.
In my opinion the only control it is worth having on an external control is Q and you already have that. Any good quality metal shaft pot should do. I would fit a 100K log in series with a 22K fixed resistor since you would never want the Q damper to go down to zero. Or possibly a 47K / 50 K log in series with a 33K resistor.
And yes it is the tolerance that is the real issue with those ceramics. Like I say, all you really need is a 0.01uF for guitar and maybe a 0.022uF for bass otherwise you end up with the pedal range extending too far into the bass or the treble. I know, I have tried all this. With a Wah Wah it is all about finer adjustments and less is more.