well i keep trying to get all the photos together.. and im nearly there just never have the time in the evenings to draw it up propperly.. so in the mean time here it goes:
Firstly remove the old sterio and the glove box.

the above photo is in relation to the back of the head unit.. (the photo was before i fully worked out the wiring so ignore the label that says CD changer as this is infact the 3 wires that control the different heights of the stock antane (sp)
Put simply i only made use of the wire for the antanne and the power, a stock toyota harness has an female interface for this plug and is later mated to a stock iso plug to provide the 12v switched and live plus a ground source free of interference.
Taking the iso plug i rearanged some of the pins leading to the toyota iso so it matched the 12v signals and the gnd signals as per the photo bellow
Ground was the far left and bottom pin IIRC.


The next phase was to identify where the amp sent the signals to the speakers so we could effectively bypass the amp with a plug and play solution.
This was achieved when we found that the top two plugs on the amp (in white) were the speaker outputs.
These plugs are male toyta harness plugs as per a toyota iso harness kit... handy eh?

I made up 8 wires about 60cm long and connected these to the back of the toyota plugs, this then ennabled me to connect directly to the speakers and run the wire back to the head unit where i then connected said wires to the iso plug that was conected to the stock power input.. if that makes sense
So the long and short (without diagrams yet) is that you ditch the stock wires that take the signal from the head unit to the amp, make a lead that takes the new signal from the new HU to the wires that come out of the amp. you then take the power from the stock head unit and feed it to the wires into the iso plug for the new HU.
I have photos of the whole job and pinouts etc etc and total costs are less than £20 all in for a complete plug and play solution with no hissing or popping..
sorry its a bit quick and crap at the moment but im at work