Chrome plastic looks cheap. If it's metal, like the anodised aluminium pickguards, it'll change the sound - messes with the pickups. Pearloid is classy - white for contrast or black for blending in. "Silver" pearl would work too - it's a lighter version of the black pearl. With black, you would probably want to change pickup covers too.
Installation of humbucker/s
One in the bridge. If you want to go fullsize, just make sure the body is routed for it under the pickguard. Otherwise a "rails" type pickup for higher output, more humbucker-type sound or a "stack" for something that still sounds like a single coil.
Black + Gold knobs
Also depends on the pickguard - you'd usually want a contrast. Chrome lasts longest out of all hardware finishes and will also match the bridge.
Black chrome tuners
The black wears quite quickly and is not environmentally sound (unless it's "cosmo" black, which is very dark gray). Wilkinson EZ-Lok from Guitarfetish are cheap and good design. Otherwise staggered height locking tuners like Schaller - which are expensive and you'll need to drill.
Dot inlay mod (not sure what yet)
You also need contrast for maple, so Paua abalone. Mother of pearl is too light. I'd leave the black.
Turn your first tone into a master tone and use a no-load pot for the second, which you use as a neck on switch to get the extra two sounds Garth mentioned (all three pickups and bridge and neck together) - only with the ability to blend in the neck pickup as much (or as little) as you like.
Alternatively, use a SuperSwitch or Megaswitch E to change the position three sound from middle pickup to neck + bridge - it's a more useful tone for me. Then you can use the second tone to work as a dial-a-split, which gradually changes your humbucker to a single coil - with every point in between. You could even get really fancy and use a cap so that it stays humcancelling, even as it becomes a single-coil.
Remove the second string tree entirely - it's not necessary and causes tuning problems. If you get EZ-lok or other staggered tuners, you can do away with both. Otherwise a Graph Tech string tree.
Nut - Big component to the tone, so I never
compromise with the nut. Any decent nut will improve tone and sustain. I like the Graph Tech Trem Nuts as they help the guitar stay in tune.
The axe has a near mint metallic black finish that I'm not too keen on changing - I quite like the fact that it's metallic.
No argument from me...