Graham
That was the exact problem I had on the guitar that i tried to from scratch.
The low E string was fine down at the pickup end of the neck, but close to the edge of the neck up by the nut.
On the high E string it was just the opposite. What I had to do was adjust the angle of the saddle and Bridge.
That made the spacing correct. However I still can't great sound out of it - too much vibration in strings. I think it has to do with poor placement of fret bars.
It was my first (and only ) attempt at guitar building..... and I did it without any knowledge of guitars at the time. I may try to build a new one this inter now that i actually understand how an electric guitar works. good luck with your project.
Have you been performing at all ? Haven't seen any new videos of late.
Take care
Jim
The price of anything, is the amount of life you exchange for it. - H.D. Thoreau
Your vision is not limited by what your eye can see, but what your mind can imagine.
Make your life count, and the world will be a better place because you tried.
"Use the talents you possess, for the woods would be very silent if no birds sang except only the the best." - Henry Van Dyke