Thanks for the info and drawings Idleup.

I started to look at doing what DW crash suggested and when I had it all apart I thought why not check the way it is already with the square method.

So i put the housing on a flat surface with a square to the side/behind and slowly rotated it until I identified which way it was off, I then gave it a little "tweak" and checked again.
I now have it perfectly square but it may still be off center, but this method works really well to get it vertical.

Going to turn up a dummy motor with a point and then slide it through the housing and see if it meets with the center of the spinner nut. If not then I will have to re-drill using Idleups method I think.

Thanks again all the different suggestions got me thinking in the right direction.