As noted on Discord, this is not surprising if you have the target decoupling capacitors mounted.
CLOCKS_FIXED should be set according to your chipwhisperer installation: if you are using the 6.0 release or an up-to-date develop branch, then set it to True.
scope.extclk_tolerance will not affect the results in any way. It is simply the threshold that Husky uses to warn you if the target clock frequency is not what you told Husky it is.
The “gain too low” error is simply that. Consider it more of a warning; increase scope.gain.db until it goes away (it’s a sticky error so you’ll have to manually clear it first). This could be because you have decoupling capacitors; however in any case it means that you’re not using the ADC’s dynamic range very well.
The last post of this thread shows what the traces should look like (with decoupling capacitors removed).