Ok well i'll try and give you a few pointers, but I don't know much about ships and the modernizing process but here is what i pointed out about the drawing itself:
http://postimg.org/image/cq4dtq9st/full/
1. I think you removed a bit too much on certain areas, especially the guidewires (not too sure about that) and the main turrets are pretty bare, might as well kept them the same.
2. If its gonna be a 90's ship, might as well remove all the 25mm stands
3. Is retaining the heavy AA mounts absolutely necessary? I mean there is most likely going to be equipment there that would be much more useful. (maybe you're going for a modernized-Iowa "look"?)
4. Since you've removed the 6.1 inch guns, maybe remove the stands for those too? Unless they still have a purpose such as mounting CIWS, SSM/AAM, or electronics
5. Searchlights are next to useless due to radar
6. Dont forget to but back the railing!
Also, nothing about the equipment on the Yamato was "useless" it all had a purpose on the ship.
EDIT: cant figure out why image is resizing, i'll try to fix it; link posted instead.