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The type of behaviour you're describing is usually caused by using Linear taper pots rather than Log and I've never had this problem using log pots. Replacing a 100k pot with a 50k one shouldn't make any difference I'm afraid as it's more to do with the ratio of the resistance between lugs 3 and 2, and lugs 2 and 1 than the absolute values of resistance.
For the gain control it's kind of different depending on each pedal, anything with a 'control' knob is using that knob as a kind of pre-gain control, i.e., it reduces the signal going into the pedal. For everything else the easiest way would probably be to add your own control knob by replacing the input with a 100k log pot using the following connections:
Lug 3 - Input (from input socket)
Lug 2 - Board Input
Lug 1 - Ground
Hope this helps.
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