Well, concerning Japanese Merchant ship losses, The JANAC report can be found here:
http://www.ibiblio.org/hyperwar/Japa....html#contents
However, the list, merchants lost to all causes is long:
http://www.ibiblio.org/hyperwar/Japa...-Losses-4.html
Japanese merchant and naval losses, listed according to which US submarine sank them:
http://www.ibiblio.org/hyperwar/Japa...-Losses-6.html
Good Luck on your mod!
Merchant ships are listed as cargo, passenger-cargo, transport, and tanker. However, there is no summary breakdown, so you will have to do the counting manually.