If it's anything like my B16, there is housing running down the full length of the downtube to where it exits by the chain stay. I just re-ran my first set of cables when switching out my cockpit, so I understand the reservation, but this isn't a difficult job. As mentioned, Park Tools has a good set of resources as does http://bicycletutor.com.
The way to do it would be to loosen the cable at the derailleur, pull the housing out through the frame to the desired length up top by the cockpit. Then pull the cable backwards out of the loop of housing by the rear derailleur well into the downtube. Then pull the housing through from the back to the desired length and cut. I left the loop by the rear derailleur the same length. I did have trouble with the cutter pinching the housing to where it was difficult to push the cable back in. Had to push a piece of wire through to open it up a bit. Maybe there's a solution for that?
For the front, it's a bit more difficult as the exit point for the housing is under the front derailleur and there's a little plastic tube that's fed around a metal bracket. Don't loose that tube.....otherwise your cable runs around a loop and is rubbing metal. Only a matter of time before it frays and fails. Same thing though...pull the housing out to desired length, then pull the cable well back into the housing in the downtube, cut, push cable back through, reattach to derailleur or brake, trim cable to desired length then and place the crip cap on to prevent fraying.
Lastly, front and rear brakes is the same. I cut several times as I was scared to cut the housing too short. I made sure there was enough room to steer the bike right and left without impinging on the stem cap with a fairly tight turn.
Someone correct me if I steered him in the wrong direction, but that's how I did it with my Felt.
**Just re-read your post and if you're going to shorten your extensions, you'll have to pull the entire housing and cable out, cut the extensions then recable the bike. Will take a bit of time, but still doable. The cool thing about the B16, and I'm assuming it's the same for the B2R, the holes at top tube where the FD, RD and rear brake enter in has a gude all the way down. You can just shove the housing all the way down the right hole and it will come out in the right spot down below. Makes it very easy to run the housing, cut to the correct length and then re-run your cables. You might have issues with the cable fraying when trying to put it back in, but since you're cutting length, you can cut the cable to give a fresh end before pushing back through. I read about putting a small drop of super glue to prevent fraying. Not sure if you can do this prior to pushing through the housing or not. Maybe someone has some insight.