Here is an image that I pulled from the web that shows how to install capacitors on limit pin inputs. You will want to do the same for all the input pins you have in use.
Brushed DC motors can also be a source of EMI, so you might also benefit by adding caps to your spindle motor.
EMI problems with Arduino Uno grbl installations are very common and can be difficult to resolve, and sometimes more than one source of EMI is present, so several "fixes" are often needed.
John