Brendan
The 250E has the small case motor, 6 speed box, longer underhang on the fork legs, different barrell (same piston), different electronics and stator, slightly lighter, different frame, air cleaner and the obvious, different swing arm.
They share with the 250D, rear shock, seat, tank, wheels and brakes.
The YZ400D and E are identical in most things except for forks and swing arm.