Made up a tool last last similar to what idelup suggested, I went with a turned point so I could see exactly how it lined up.

My starter housing was vertical but offset one way as I suspected. see picture. I was able then to tweak (bend, push, hammer) it until I got the point lining up in the middle of the spinner nut.

Made the tool 24.3mm dia and is a nice sliding fit in the housing. The small diameter is 14mm to fit through the hole, other dimensions are not that critical.

Tried my starter and it lines up lovely now, new problem was it was too far in as when I tightened up the starter bullet cover it pushed the motor in too far, (I think the new motor I have the bendix is further out on the starter shaft) ended up fitting a 3mm washer under each of the housing legs and then had to align it again.

Have it all fitted in again and might get to fire it up tonight.