(So you must be tuned BEAD, right?)
Replacing the saddles is not difficult, it just takes a while to disassemble the bridge and put it back together. There is no reason to replace the entire bridge. You can just order some new saddles, either blanks to slot yourself, or possibly (not sure) have Alembic slot them if you provide them with the necessary details.
There is no rule about where the slot should be positioned on the saddle. They are all cut by hand, considering string spacing, distance from edge of the neck, etc. Sometimes they spread out toward the sides, others bunch in toward the center, and some may just be shifted to one side. However, yours does seem a little strange, in that it would have put the BE too close together, and EA far apart. If you like the spacing after re-slotting the E, then that's fine.
As for the width of the slots in the nut, as long as they are somewhat V shaped, or have a small enough bottom in the U that the strings fit securely, then that's also fine. You want the slot to have contact up the sides of the string (ideally, a full half circle). If the strings are mostly just sitting on the bottom of the slot without much side contact, then you might notice a slight improvement with a better fitting nut, though it will only matter for open strings. You can certainly get a new blank for the nut, and fit it yourself or have someone local do it for you.
-Bob
