How to improve accuracy
I am printing a part I designed in Fusion 360 and sliced with Prusa Slicer 2.9.2. I am using the latest firmware for the MK4S (I upgraded it from an MK3S)
The MK4S boasts dimensional accuracy "often within to .2% of the target". I had this accuracy before I upgraded, but I am not seeing this now, so I am unsure if it's a slicer issue. It consistently prints the exact measurements each time (though off by the same amount).
Here is the design, and here are the calculations of how off they are. 
The hole is off by more than .5mm (it's already 1mm bigger than I need it)
The widths and lengths of the oblong slots are off. The measurements are already .2mm wider than the aluminum that needs to fit in there, but these are .4mm shorter in both the x and y directions.
Height, I can deal with, and that's not off as much.
I measure the distances in the slicer as it sits on the plate, and they match my Fusion 360 measurements.
Something is either happening mechanically with the printer(though I have run the calibration many times, and the print output is consistent) or with the slicing.
Any suggestions other than messing with my design to make it .4mm larger?
RE:
I figured out the issue after printing out an exact 10mmX20mmX30mm cube with perfect results. I found it odd that almost all of the "holes" were essentially off by .4mm. As I felt around the piece, the first layer appears to "squish" out a bit as it is layered on. I think this is referred to as a boot, approximately .2mm from each side, which totals the .4mm. I chiseled off the excess and found underneath an almost perfect fit. Still tight, but still within tolerances I assumed, and nothing a little forceful encouragement with a rubber mallet couldn't handle. It's only an issue with holes created from the first layer, which makes sense.
RE: How to improve accuracy
This might be 'elephant foot compensation'? Under expert print settings/layers and perimeters/slicing/...