It's been a bit of a busy month but I am still here, working on the reprap when I have a few moments spare time. I managed to get some firmware onto the extruder which was nowhere near as simple as I expected, but I got there in the end with the aid of some helpful bloggers. The secret, hold the reset button on the board for 10seconds after you clicked the program button from the arduino software. Something to do with different types of atmega chips, I didn't read in to it too deeply as I was just rather happy it worked!
Apart from that I still need to finish the cable routing and order a replacement component for an optoswitch. The optoswitch I managed to break by connecting it the wrong way to power and ground, I'd like to say it wasn't my fault but it turned out I was using the wrong version of the motherboard schematics as a reference. Never mind I found a replacement on Farnel (optoswitch) so all is good.
I'm happy to say that it looks a fair bit tidier now!