Could be the coupling caps...that would be my first suspicion after the supply caps.
Might also be a "playing position" type of thing - some types of guitars, especially semi-hollows, can really get some odd "ghost note" problems as a result of some resonant frequency thing, i guess (i dunno, I'm not too familiar with the problem, thank goodness!). Try changing your position in relation to the amp and see if that helps, or maybe a different guitar. If it still does the same thing, I'd redo the coupling caps.
As for lower value caps, if you feel confident the rest of the amp (notably speakers) is up for the increased low-freq response, I wouldn't see why not. I bet the originals had a higher value to account for leakage anyways...just have to make sure you don't go too low.