Yamato's deck were natural wood, so you're correct in using the color you chose.
I typically build the superstructure, attach the PE, and then paint when I'm doing an IJN subject. Since the Japanese Navy had no specific deck color (other than lino), it makes life easier to attach everything then paint. Once that's done, I'll attach the superstructure to the main deck level.
This is, of course, different from the way I model other ships from other navies.
Jeff