Well, after spending a lot of time thinking about how to fix it, I resolved to do the following.

1. Get a new body and do it all again;
2. Get a proper drill guide and test it on some scrap wood;
3. Remeasure everything;
4. Use the old body (when experiments have finished) by filling the holes, painting it and using a top loader bridge ( which is the fender bridge I use as a drilling template.

This has the absolute beauty of 2 competing ideas. They being, I get to do a redo on my string through bridge, with a proper drill guide and practising on scrap to make sure I have this right. The second idea is that, when I get another neck and some pickups, I will have 2 telecasters and I can compare top loader with string through.

I think you will all agree that my plan is exceptionally sensible.