Your integration time is way too low, at the minimum of 0.25.
You should be using a much higher value. That will be a key issue, as you have a number if invalid probe readings as the probe is struggling to get valid readings.
(0.75 is probably the minimum - 1.25, or higher, will be better)
Also, a drift value of every 10 patches is way too short - 100 is a more realistic value.
You should also be using AIO mode with the i1D3, as per the above link (assuming the i1D3 is a RevB).
And if the white point is spot-on, you should set the display to the desired peak luma value (100 nits) as there will be no reduction when the LUT is made. That will only happen if the white point is not accurate, as the user guides explain.