The best route for a turbo would be 3 in downpipe, a 3 in straight pipe (no cat), and 3 in piping the rest of the way. Period. Backpressure works against the turbo, slowing down spool up time and lowering boost. Imagine you are holding a little propeller in your hand. You blow on it to get it spinning. Now you blow on it the opposite direction. What happens? Yes, thats right, it slows down. The same holds true for turbos.
This is physics, plain and simple. The Ideal Gas Law states that gas temperature, pressure, and volume are all related. Compress a gas (reduce the volume) and pressure and temperature goes up. Let it expand, and temperature and pressure go down. Increase the temperature, and the pressure goes up (in an enclosed space) or the volume goes up (it expands). Finally,
gases want to flow from a high pressure area to a low pressure area, and the greater the difference, the bigger the push. This means that the greater the pressure difference from where gasses enter the turbine to where they exit, the faster it is going to spin the turbine.
For a more detailed explanation on how turbos work check out this page:
http://www.dsm.org/menu.epl?item=363