My latest mudbunny build was very noisy so I subbed a 470uF electro for the 100uF that was spec'd. That alleviated much of the noise problem nicely. My question is, will there be any affect on the guitar signal's sound by this increase? I assume no as the power section should not be in the signal path. But if that is the case what is the "give and take"? What do I lose or affect by this increased amount of capacitance?
You lose nothing. You only reduced noise, which is good. ;)