I see colin2121 is making the exact same Left Handed Jazz Bass as I am.
It's a bit late now, but this is how I set up the bridge position.
I used some cotton kitchen twine, (which is normally used for tie-ing up roasts and the like), because it doesn't stretch.
I just used Blu-Tak to secure two lengths of the twine behind the nut:
I marked the position of the 12th fret with a Texta pen, and then doubled the twine back and marked it where it passes through the nut. (It's better if you can get someone to help with this). That way the first mark should be at exactly half the scale length, and the second should be twice that, that is, the actual required scale length:
I added some weights to the other ends of the twine so it hangs over the end of the body, keeping the twine taut:
Then it's a simple matter of dropping the lengths of twine into the relevant slots on the bridge and moving the bridge around until the twine lines up best with the outermost pickups, and the Texta marks line up with the centred adjustable bridge saddles. I'd recommend you just drill two pilot holes at first to make sure the bridge hasn't moved, and re-check the alignment before you put the rest in.
By the way, I'm writing an article for Silicon Chip magazine about my experiences with this project, which is why I haven't touched the headstock, because, you know, Fender and their friends get a bit tetchy about what they see as their copyrighted designs!
That's actually another reason I went for the Natural Wax finish; if you do any subsequent modifications to the woodwork, it's really easy to re-finish it, which is not the case with lacquered finishes.