ive done this many times, it can be done with the servo on, just unbolt the master cylinder and move it a few inches to the side, feed a few connectors through at a time, then go into the car and pull them through, do this a few times and they all will come through, as for the back of the fusebox, are u sure u have fully pulled out the plastc bar what runs through the middle of the fusebox,
on my gti, i swapped my 8v to the 16v, i only needed to change the engine managment side of the fusebox, all the dash wires and loom stayed in.
i can change the whole loom on the engine to the fusebox from disconnecting the old and installing the new loom in under a hour, so its not to envolved really.