Thanks for all the advice guys, I'll have a play around and see if I can sort this properly.
I'm talking about my fat tele, put in a humbucker sized tele bridge, all the holes lined up perfectly and saddles are in the same (roughly) position.
Lowering the pickup doesn't seem to help.
It's a pain, but the rest of the strings are in perfect tune, but not the low D. Even when the string is tuned to E it works, but when in drop D notes are miles out, even by ear.
To recap, low string is fine when tuned to E, tuning to D can't intonate at all, and it's super noticable.