I doubt the transistor change would have an audible effect. You'd be better off changing all the higher rated resistors (anything 100K or higher) to metal flim. Carbon films at high ratings tend to be a little hissy.

Keep in mind that you've doubled the pedal's gain with that change of the 4.7K resistor to 2.4K, and that doubles the noise, too, when the gain is dialed up. So you're fighting physics, to some extent.

I wouldn't worry about that 0.02 cap. It's at the start of the input buffer and I've never seen any mention of it being tonally important.

Can't comment on that 8.2K resistor; that's not a rating I've encountered in a TS.

BTW, your bass didn't increase with that switch to a 0.1uf cap--it just compensated for the 2.4K resistor. The two form a frequency filter, and when you cut the one in half, you have to double the other to keep the bass response the same. If you really want more low end, increase it to 0.22uf.