Re refurbishing the shift knob ...
The knob can be removed fairly easily (search on here for instructions) and the 'metal' part prised out, there's been a few threads on here where people have repainted them successfully.
You can also buy replacement leather boots on ebay, e.g
https://www.ebay.com/itm/FITS-PORSCHE-986-BOXSTER-CARRERA-996-LEATHER-GEAR-KNOB-SHIFT-BOOT-SKIN-COVER/390774072560?fits=Model%3ABoxster&epid=1790018853&hash=item5afbf324f0:g:rO4AAOSwk1hZ8aJV
(not recommending that vendor, just the first one that came up in a search, you'll find more if you look around.)