Today I bit the bullet and moved the Y axis stepper motors to the outside of the carriage. This has been annoying me for a while given that the brackets always get in the way and I have to work around them.
Rather than mounting the belt on the top I chose to mount them on the bottom. This enabled me to get the mechanics out of the work area. It also allowed a more compact implementation.
By moving the motors to the outside I gained a few extra centimeters of print area and the X gantry will not bump up against the motor gears.
I have looked at many mods but went with printing motor mounts from thingiverse http://www.thingiverse.com/thing:27860.
I could have used standoffs but chose the printed solution.
I then cut a small notch in the side of the frame to string the gear pulley through.
Here are some before and after photos