wheel / fender flares
 

Do wheel /fender flares serve any aerodynamic purpose? Would it be better to remove them and put rear wheel skirt accross flush with rest of body .. or to install wheel skirt flush with widest part of the flares?

Don

fender flares
 

This falls into the 'it depends' category.
Front flare performance would be governed by flow coming from the nose.If the air is 'dirty' it doesn't matter,the flare would be embedded within the turbulence.
If the flow is 'clean' the forward flare may 'kick' the flow outwards to avoid the wheelhouse,re-attaching near the wheelhouse rear flare.
These flares also help with splash and spray coming off the tires.
The rear flares may be of no import if the flow coming at them is also 'dirty',in fact they won't work if the flow isn't clean.
You ought to tuft test the sides of the vehicle before you proceed to do anything,to establish 'where you are'.
Since aft-body mods are dependent on a clean fore-body see first what's going on.
If you like what you see then the skirts are warranted.And just because of their trouble to 'remove',I'd be inclined to just skin over what's there rather than cut away the body.
Follow basjoos lead with his AeroCivic.