I'm in the process of the same thing but I'm re-routing mine to eliminate the coupler up top.....the best way is to cap it at that coupler and in the valve under the MC. typically the correct way would be to run new lines and make the path with no couplers but if is the route you choose(i would do it too if my lines werent rusted) then cap it, otherwise you have all that extra space to have leaks and air pockets and bad brake pressure
hope that helps