The AFR lean spike investigation continues.... Thanks to plohl for the telephone support on this issue!
Data showing the AFR lean spike and the TPS value. Note TPS is logged at 20hz as this is the limitation of the Haltech CAN. Photo from the session shows the AFR lean spike happening coming out of T6 despite the even throttle (green trace), the lean spike (red trace) continued to develop. After the change from 4 to 5 (blue trace).

As mentioned, Shane helped out on Saturday and Sunday with advice, starting with checking the timing and locking the ECU at 10°. Whilst not getting to lock the ECU at 10°, I was able to get the timing light to work.
Before locking at 10° I started to upload a few changes to the Racepak IQ3 dash and logging changes to the Haltech PS1000.
A test of the new dash settings showed very strange behavior with the TPS under certain conditions. When the accelerator is pushed quickly to 100% it was fine, but put too much pressure on the pedal and it started to get very 'noisy'. Hmmm could this be the cause of the issue?
The car is tuned from the TPS sensor hence if this data is 'noisy' the car will try and quickly change fuel/timing based upon the relevant table (thanks Shane for explaining this).
What the ECU saw... If the pedal is pushed quickly no issue, but slow and steady causes the 'noise'.

Zoomed in of what the TPS is 'seeing' hence with the ECU is matching fuel/timing to...

Long story short, a stop was put in (24mm) to stop the pedal traveling too far and avoiding the 'noisy' part of the TPS. Still need to confirm that the ITB's are opening all the way, but most of the 24mm of previous travel was bending the pedal assembly (amongst other things).

The sensor was then re-calibrated and tested...

Is the problem fixed, no idea until next track day. More than likely the ITB's will need to be rebuilt, the TPS replaced, new throttle cable installed, pedal box and a new tune. Then it will be on to the next issue...