If I position the bridge in the rout so hole is covered (ignoring the screw holes and leaving pickguard off) I can get a 648 scale length with the saddles at the half way position on the low E. So as the bad screw holes are hidden by the bridge I guese I can drill new ones.
Well that's a good alternative. Did you have the pickup in the bridge when you test fitted? You want to be sure you can get the same bridge position without having to alter the routing.

Further once I fit the pickguard I can not get scale lenght so will either need to take a bit off it or alternatively go with a neck ring and switch plate to reveal the grain. The only aspect here is thinline control cavities are at an angle to the neck while normal teles have the control rout aligned with the neck. Can anyone see an issue here I am not seeing?
When you listed your intentions in your OP, I immediately presumed you would just customise the stock pickguard.
The way the pickup and cavity routing is in that model, you can easily make a standalone control plate out of the pickguard (or any material of your choosing).
If you go that route, we can help you through the methods of cutting, shaping, bevelling the pickguard material.
You could even make your own matching neck pickup ring. But I can see how a premade chrome one could look good on there as well.

I totally agree with trying to minimise the amount of the top that's covered up.