Looking at that schematic I have to wonder if much
of the EMI problem isn't of your own making.
There's EMI, and there's EMI. Thinking only in voltage
mode you might think those huge shunt caps are a
good idea. But what you're doing, is ensuring a fat
slug of current on every transition since you put them
bare to the MCU output. Add any loop-area to that
and you've got a pretty good radiator of energy.
A series resistor between output pins and shunt cap
would help that, some. On the other hand I kind of
doubt that voltage-mode risetimes are fast enough
for a ferrite bead to knock them down much, if you
are putting them in place of those shown inductors.
I think you'd be better off with a close-in RC filter
with a corner about 3MHz, where C includes the
driven load.