Yet another ballache with Exchange 2003, here's a quick summary to perform this 'simple' task.

Firstly get pfmigrate.wsf , for some reason most documentation pointed to the CD which was annoying, the latest version is available here with the exchange deployment tools

So let's try and migrate those public folders:

pfmigrate.wsf /S:elephant /T:spider /A /n:100

This should migrate from elephant (source) to spider (target) with the /A switch adding the target server to the replica list of folders and with /n:100 modifying 100 folders at a time.

First error:

The token supplied to the function is invalid. ID no: 80090308 Exchange System Manager

So upon running pfmigrate again I get presented with another error,

Failed to enumerate public folders.
Access denied
Facility: Win32
ID no: 80070005
Microsoft Exchange Management

The fix for this is again simple, remove basic authentication on the exadmin folder in IIS leaving only integrated auth on.