Brake lines were never meant to be run inside the tunnel. They ran down the lower side of the tunnel inside the car.
Fuel line can be a bear to re-do. You can snake it inside the tunnel. I usually like going from the front to the back. You can remove the shifter and the e-brake and use some heavy zip ties to secure it along the way. I would secure it at the front, at the shifter hole, the e-brake access, and the rear. I would also slit some rubber fuel line and use it as an insulator where ever you zip tie it. You will need VERY small hands and LOTS of patience.
You can also cut access holes in the tunnel and weld them closed after you attach it.
If yor buggy is a street buggy you should really consider running them outside the car. Its done on many cars like this from the factory.
To shorten the cable see this thread:
http://www.thesamba.com/vw/forum/viewto ... shortening
I haven't tried it but it looks slick.....and cheap.