Efficiently? Definitely not by running the over the Williamsburg Bridge. You diminish the efficiency of the , , , , and that way.
How does continuing the via the Williamsburg Bridge reduce the need for shuttle buses? There is still a lack of service between West 4 Street–Washington Square and Broadway Junction. By running the over the Williamsburg Bridge to get to Broadway Junction, you think shuttle buses won't be needed (if they were even needed in the first place)?
And then after the fact, you have a bunch of trains in the wrong places. If you've ever worked with any kind of inventory, you should know how much of a pain in the ass it is to work with things when they are not where you expect them to be.