I did a bit work filling the hole under the bridge with match sticks and super glue. I drilled a new grounding wire hole and mixed in the dust from that hole with the glue to fill the surface. Sanded flat it looks okay - time will tell I guess when I try to drill the string holes.
I then worked on locating the bridge. I marked out where I thought the centre line of the body is and got the rough scale length. Then I tried to centre the bridge using the two Es. However when the strings were centred on the fret board the bridge was about 2mm north of my centre line.
To double check I loaded the pups into the pick guard and rested it on the body where I though it should be - the guard has long edge that buts up to the neck so its easy to locate. It seems like either my centre line is off or the neck is pocket is not quite straight in the body, but the poles of the pups seem to line up prefectly.
I took my centre line using the neck pocket, the pup cavities and the largest width of the body. So it's more than likely I'm off with my measurments.
If someone can take a look at the pics attached and let me know if I'm missing something obvious? But it looks good to me?