It would be worth checking all the voltages as per this thread.. (unless you've already done this)
http://www.mr2australia.com/mr2play/tm.aspx?m=39415
particularly the NSW (neutral/park switch signal) as the motor wont crank without the correct signals.
 
 

The motor cranks but I get no spark or injection

the security light just pulses as it would if it was immobilised
 

Do you have the unlock warning switch from the original key barrel wired into the transponder ECU?

TomsMR2
Do you have the unlock warning switch from the original key barrel wired into the transponder ECU?

Yes I have the switch in place and hooked up.

Tom, did you do the wiring yourself for the 2GR?
 

PMd

You can ground the ksw pin3 on transponder ECU to test this, without this the antenna on the Aurion ignition barrel does not energise

I did my own wiring and it started first time
When you turn ignition on does the accelerator pedal operate the throttle?

I will try putting it straight to ground and see if that works.

I will also test the pedal

I really appreciate everyone's input. Going to pull some late nights to get this thing working.
If anyone has any ideas, please share them. I'm open to anything at this stage.

 

If accelerator pedal does operate the throttle then you know the engine ECU is basically working ok.
I was able to test that even before I wired the immobiliser circuit in.
The constant flashing security light is surely a sign the issue is immobiliser related, as I think that works partly independent to what the engine ECU is doing, I know on mine I only have the ksw wire grounded to chassis at the minute as I have not finished my swap but if I disconnect it the security light starts blinking

TomsMR2
If accelerator pedal does operate the throttle then you know the engine ECU is basically working ok.
I was able to test that even before I wired the immobiliser circuit in.
The constant flashing security light is surely a sign the issue is immobiliser related, as I think that works partly independent to what the engine ECU is doing, I know on mine I only have the ksw wire grounded to chassis at the minute as I have not finished my swap but if I disconnect it the security light starts blinking

Yep it works as soon as power goes to the box as far as I am aware