I couldn't see from your photo which way you were running your Spindle, when leveling. 1.5KW spindles are really quite heavy and it worries me that you might be getting twist on the X azis.
I was running pocketing along the X axis. That is what is worrying me too. I have put it up for sale. I will be downgrading to a 800W water cooled one.
The Z and X are not perpendicular. I used some shims on the lower part of the spindle. However, it seems there are a bit bigger than need. I will try different shims and test again. The difference in heights between the layers are reduced drastically.
I used one of my feeler gauge to adjust the spindle and tested it on another MDF. Results were much better this time.