Am considering swapping off the chrome side 'tubes' and going for a more subtle black side step (not the deployable ones). Question is, I've got a set of genuine LR front and rear mud flaps to fit, will these fit with the black steps/skirts, or will i need different mudflaps too?

Genuine LR side steps require a specific set of front mudflaps which include a section the side step locates into, rears are the same either way I believe.