I managed to fit all of the laser cutter components back into the box again. Getting the cover on was a significant step towards seeing where everything will fit. Sure there are cables strewn all over the place but they can be routed round as required, finding the space for each of the boxes was the important part. The high voltage PSU and the Stepper motor PSU all tuck into the gap on the right hand side of the case. The stepper motor drivers and control board can fit along the front edge of the machine. Now I just need to drill more mounting holes and shorten a whole bunch of wires.
I have totally managed to remove the lower half of the machine and the only thing I've lost is the ability to engrave boxes (or at least I have to engrave boxes slightly differently)