In some of the other forums or under search you can find a list of Japenese Naval Bases. I've found some at Kobe, Truk Lagoon, and Rabuel and I've heard rumours of them being seen at Manila. Haven't checked that on out, there seems to always be a task force in the Celebes Sea and or Bismark Sea untill mid 1944. As for sinking a Yamato Class, if you can find one, it took me a while, 7 - 9 torps is normally pretty good. as for week spots, right in the middle under the command bridge is where they welded the to seperate sides. If you can hit about 5 meters down under the forward guns twice you usually rupture the forward magazine and make a big ka-boom!!!!

then one or two more in the hind end, usually under the rear turrent marks the end of the ship. Hope this helps.
By the way, welcome to SH4 and Good Hunting!!