its a very long process to completely rule out the entire audio harness but you will be able to achieve the best sound doing so. to do so you can use the following
-head unit with 6 preouts
-head unit harness adapter
-a 4 channel amp
-a mono amp (for use with single sub)
-atleast a 4 or 0 gauge amp install kit (power, ground wires, inline fuse holder) depends on what amps and sub you use
-signal wire if not included with amp kit
-power wire junction box
-some 8 or 4 gauge power wire (again depends on what amps etc you use)
-3 sets of rca cables
-a lot of speaker wire
-front speakers (components for front for mach460)
-rear speakers
-misc tools and wire terminals
Now hooking up the radio is pretty basic. you splice in the harness adapter and plug and play. the rest is simple but very time consuming. find two mounting spots for both your amps. I mount mine of the back of reat seat. some people I know have made custom mounts under the rear seat and others have mounted them under the front seats. its all preference. run your 4 gauge wire from battery to wherever you mounting your amps. run the signal wire and rca's from back of radio to where amps will be mounted. find good ground for both amps.
all this will be easier to do with the interior of the car out BTW
run speaker wire from the 4 channel amp to each speaker location in the car. hook up all the new speakers to the freshly run speaker wire. take the 4 gauge power wire to the junction block and then run 8 gauge or 4 gauge (depending on what amps you are using) from the junction block to each amp. ground each amp. attach signal wire to each amp. attach all rcas to both amps in correct spots (front/rear outputs from headunit to 4 channel. and sub output to mono) Hook up your sub to your mono with speaker wire. intsall fuses. then tune your radio settings and amp settings.
Now this is a very breif description on how to do it. As far as what you use for products the head units, sub, and amps are all personal prefference and based on what you can afford. you get what you pay for. some on here are going to swear by certain ones and others will differ.
I myself have always used alpine head units. A jl audio 500.1 amp for my jl audio sub. then I use alpine speakers paired with my 4 channel alpine amp. As far as wiring I prefer Monster for my rca's. heres a link to some I use.
Monster Cable MPC I204 4c 5M 16 Feet 5 Meter 4 Channel Interconnect RCA Cables | eBay
IMXLN2C 5M 15' Monster Cable 2 Channel 16 ft RCA Wire | eBay
These are a couple. obviously there are better and worse stuff out there but I personally have never had any issues with monster and ive run numerous systems with them in multiple cars. the price is very decent too.