I've had some luck with the Y axis now. I loosened the gib strip which helped a bit however it strikes me as being too loose now. I adjusted the backlash adjustment and now I've got 2300mm/min on the Y axis, but about 0.2mm of backlash instead of 0.065mm.

Good news with the Z, 4600mm/min with 1:1 pulley!!!! It will do more if I change the motor to half stepping because the computer is limiting the pulse rate I can use at 1/4 microstep, however 4600 is plenty fast enough for an axis that's only got 92mm travel. I'll keep it at this ratio to preserve torque for drilling etc

So to summarise:
X, 2520
Y, 2300
Z, 4600

Overall I'm very happy with this - can't wait to start machining things again! Thanks for all the help that's enabled me to do this...

Also, could someone point me to a simple program to import a 2D .dxf and generate g code for '2.5D' milling from it?