Dave, Definitely listen to ESjaavik. Disassembling a stepper motor will definitely result in lower torque. I don't know if you are demagnetizing it but it is extremely difficult to realign the gaps between the stator and the magnets. Don't ask me how I know this, ahem.
You say that you measure a zero resistance among two sets of three wires 1,3 & 6 and 2,4 & 5.
This identifies the separate coil phases but you are going to have to take more accuate measurements to determine which wire is the centre tap... although its been my experience that the motor manufacturers DO try to make it easy for you.
So my guess would be that 3 and 4 would be the centre taps.
HTH Gary
embrace enthusiasm to accomplish the task
Gary Davies... www.durhamrobotics.com