Yup I've got that the big black one I had on the starter needs to go to the gearbox. The alternator was pretty easy i think as the wires would only connect one way although I only had 2 wires and some pictures I've seen people have 3 wires? I think the big one to work out now is which one is the chassis earth, which one earths onto the head, and should I have an earth strap somewhere for engine to chassis?

The 3rd wire will be missing from yours as that one normally goes to the choke which your engine didnt have as it wasnt on a carb

Ah that explains the alternator then. Here's how my starter connections look now, can someone confirm I've got this right now with only 2 wires connected to the starter instead of 3?