As yours is a Euro3 you can blank them off and the EML won't come on. I've got an EGR bypass pipe which does away with the whole component (and provides a take off for a boost gauge).

As has been said panel filter, decat, Airtec intercooler, and a good remap from the like of Evolution Chips will see you with plenty of torque. I tried a Bluefin on mine and noticed no difference whatsoever other than a lumpy tickover!

If you want to improve the car Focus ST front brakes are a straight swap and are a lot better than standard.