Yes a flow bench sounds good...BUT it is used to messure flow that is constat, not pulsating. It is a great tool to check for flow restrictive shapes and surface finishes on the ports, etc.
The length of the pipe be it exhaust or intake, works like a chamber to create an airspring pulsating at the rhytm needed to feed the combustion chamber and to pull the burned gases out at a certain rpm.
So no. I don't think a flow bench will give you the answer to the lenght of pipe needed.
It would be like trying to fine tune a classic church organ with it. The lenght and diam and shape of the pipe will give you a note. You just need to find out what note is the one that makes your engine sing(at a certain rpm). And yes trial and error might be the way to go.