1. I replaced the switches in mine with gateron blacks, no issues whatsoever. The stock PCB is fine Imo, but I did install a new controller when I did my modifications.
2. See 1.
3. Personally I would recommend some cherry profile keycaps. If you have your heart set on blanks, I recommend a set of gateron PBT blanks. I am not sure who is selling them these days, but I'm sure it won't be too hard to find a set.
As for the cable, Pexon makes a cable that will work but it uses a custom connector. So as long as you aren't too concerned about it not being mini-usb I would go that route. You could do the mod yourself and install a female mini connector, but afaik it may take some hacking to get a housing around the connector. Other option would be to just use shrink wrap if you don't mind the look of it. I can't speak to painting the case as I haven't done this, but as long as you thoroughly prep the case you should be fine with most paint.
edit: Looks like
kbdfans sells the keycaps. Gateron is the manufacturer, but EnjoyPBT owns the molds.