Well that’s not good, it’s 50% worse, or so, than your previous deviation of 0.02".
You changed a lot of stuff at once… not sure what to suggest.
I suppose starting with confirming no-load positioning is accurate would be the place to re-start. You mentioned being off 1mm from square, but nothing about X and Y travel distances as you had before. I would be using a V-bit to poke some holes at the far extents of your machine travel and measuring them.
As an aside, it’d be great if everyone could stop bouncing all over the place with imperial and metric units and units of time in this thread. Heck, even consistency in units within each single post would be an improvement.