This printed perfectly.
I then taped on my cleaned copper board (Cif and green scourer again) and put it through a cheap home laminator machine.
This worked really really well. The toner transferred perfectly to the copper, and the sticker paper was left completely clean. It seems to have bonded well to the copper, so I will have a go at etching the boards soon.
This time, I printed out the PDF version and measured the printed PCB (49mm). I then zoomed in, so the tracks were filling the whole screen (in the PDF reader) and took a screenshot. This screenshot can be cropped to the edge marks, and flipped in GIMP, and GIMP offers specific print options to print out at exact sizes - i.e. the size measured earlier. This worked well (apart from a minature mouse pointer appearing on my PCB tracks!)
Single Sided Makerbot Stepper Driver board
First task was getting to grips with Eagle, and downloading the .brd files from the RepRap repository. The biggest problem with the mix of through hole and surface mount components is that the pads end up on both sides of the board - the through hole pads are on the bottom, and surface mount on the top.
I loaded up Eagle and mirrored the through hole components onto the other side of the board. The plugs are now pointing downwards (not ideal) but at least the pads are now on the top side. Rotating the connectors by 180 degrees helped match the tracks to the existing routes.
This left lots of messy tracks on the board, but a bit of work tidied them up. I then went to work moving via's (that would now have to be wire links) and moving the via points so they are not underneath the surface mount components, as I'd have to through-hole solder them. I'm no circuit board designer, so I went with moving the components as little as possible, and re-routed the tracks to avoid or shorten the vias where I could. Straightening the vias helped avoid crossing wires, and some of the connectors could be connected directly.
I printed off the PCB and transferred it to the copper. If it etches well, and I can drill some holes without ripping all of the tiny tracks off the board, it might be worth getting some components to build up a version.
[Edit - here are the eagle board files for anyone who's interested. Probably there will be later versions that might actually work.]