Exhaust systems are designed with many considerations in mind.
Other than the average flow (DC component) there is a significant
pulsating (AC) component. Lengths of tubing acts equivalent to
inductors, cavities like capacitors, and the combinations like
filters. And there is always a resistive component...

Study the layout of the VW car exhausts: First a length of tubing
then a resonator, then another length of tubing, then a muffler
and tailpipe. This is equivalent to two low pass filters in series.
The objective should be to copy one or both of these.

Practiacally on the vanagon it's possible to match the first
length to the resonator and then put on the muffler. For some
layout ideas see the pictures on:

  http://www.cs.jhu.edu/~jager/vw/engine/Diesel1_9swap/

If one wants to put in both components the exhaust would first
have to be routed under the mid section of the van, then a resonator
then a go back towards the rear, rear muffler etc.

For performance (best scavenging) it is most important to match the
first length of tubing after the engine.

Good luck,
Martin