rail pass can be very helpful if you plan on seeing a lot of Japan. If you are planning to stay in one area and have someone around to drive you or show you around you probably wont need the rail pass. Taxis are pricee here, freeways are tollways and can get pricee real quick, trains are cheap but not everyone can stand the rush hour crowds. Everyone's situation is different but in general trains are the easiest and cheapest way to get around.
Renting an apartment is not very likely here especially since you do not have a residence card, address, etc... However there are plenty of hostels and cheap places to stay. If you are looking for places to stay or for more info on how to get around or what places are fun etc... I suggest you take a look at
www.gaijinpot.com in the forums.
www.japanguide.com (not sure if that is the exact addresss just google japan guide)
Is also a helpful site.