I just put a Seymour Duncan Hot Rod set of humbuckers in my Jackson.

Id like to gut all my electronics and wiring and put all fresh parts in there. 

Will need one volume and tone and a 3 way switch. Might try to get fancy and coil split mu humbuckers since they have the wiring option to do so. 

Where is a good place and what brand is the best when it comes to guitar electronics?

Stewart MacDonald is a great place to get lost -- like a kid at Christmas ....

http://www.stewmac.com/

CTS for the pots.

Switchcraft for the jack.

CTS, or Superswitch if you have a blade, Switchcraft or Freeway if you have a toggle, for the switch.

A good quality paper in oil repro or Mallory 150 for the cap.

Other places to check:
www.amplifiedparts.com

www.tubedepot.com

http://www.mojotone.com

Wiring diagrams:
http://www.seymourduncan.com/wiring-diagrams

Yeah, CTS and Switchcraft.  

I got all of my electronic parts from RS Guitarworks, and used their paper in oil capacitors, and their "SuperPots" for the volume controls.

Don't go overboard on the tone capacitors by getting the most expensive ones.  It does not work any better than regular capacitors.

Some mistakenly believe or are told that tone capacitors are inline in the signal.  These are not.  These capacitors bleed frequencies to ground.  What frequencies depend upon the capacitor value which is more important.

You can't apply logic to the search for TONE...  LOL

I agree.   And if if there is any difference in tone, it is so subtle that I can't hear it. Especially after you run it through all sorts of effects pedals.

On the other hand, there are exactly two capacitors in my Les Paul, and I've only changed them once in 30 years.  So I figured why not splurge, and spend a few extra bucks....because they just look cool, if you ever have to take the cover off.

A good link about the non-issue brand name is in selecting tone capacitors.

It's configurable with dip switches; selectable auto ranging 250/500K pot value for coil splits, modern/vintage wiring, treble bleed, select any combination of 4 capacitors, etc.
Toneshaper kit

Here's a link to the instruction manual pdf
http://pdf.toneshapers.com/ToneShaper-Instruction-Manual-NG02.pdf

For toggle switches, check out the Dimarzio toggle switches. They're fuckin awesome. You can either buy them through dimarzio, or you can buy them through Ernie Ball customer service. Ernie Ball ones come with a circuit board attached to make it easy to solder pickups on. Also makes them easier to change in the future and makes your wiring look good. They are pricy though. They're like $30 through Ernie Ball. Once you change your pickups, you'll want to do it again in the future.

Check out bournes volume pots. They're by far the nicest smoothest pots out there imo. Also, Belden guitar wiring.

Some of this is a bit pricey, but if you want top notch stuff, I think this is it. And if you're feeling bold, you could get special graphite paint to line your electrical cavity. I believe they sell that at stewmac.

Not sure if your Jackson has a pickguard. I've ordered custom pickguards through Warmoth in the past. It's been a while since I ordered one though. I imagine theirs more shops out there now. That'll help you keep your install clean and sharp looking.

Great advice, I prefer CRL for blade switches, I use most everything else you mentioned, except for the caps, I like Orange Drops.