What's with the traffic circles? I'd ask you why it smells so bad, but I know that one. The whole state is built on a giant landfill. Do you get pulled over if your "NO FEAR" sticker is expired? Why is the ocean so nasty in NJ?
Palm- Muting can get you a nice upright sound, with the same drawbacks as Richenbacher pointed out. I'm not sure about the eq. Flatwounds would help too, I think.
I agree on the first two points. I think it's ok to go barefoot if you want. Dub Poet Mutabaruka never wears any shoes, ever. Barefoot is spiritual to a lot of people, so is music. If you always wear shoes the whole world is covered in shoe leather.
I bet it's a rosewood fretboard. This can happen when the fretboard loses moisture and contracts. It doesn't happen with Maple. You can apply linseed oil on it to prevent further problems
When you guys use a "buffer" or pedal to raise the volume, I guess you put it at the end of the chain? I have a Boss EQ and also a Sans Amp that would work for me I think