Right, it certanly isnt an easy job, but it isn't going to be amazingly difficult either. Since when you have the head & block together you'll essentially have a MK2 1.8 GTI engine, the ideal starting point is getting hold of the complete engine loom & ECU from a post 90 spec MK2 GTI. Post 90 is easiest, since the plugs on it will be the same as your fusebox. I think you'll need a MK2 GTI distributor as well, I'm not sure if the 1.8SPI one will work, but it may do.
You'll need to changew the fuel pump as I doubt the SPI unit will be up to the job, and you might have to replace the fuel lines with MK3 GTI items as well!