First off, don't bother searching on the net. They only have expensive apartments and the cheap ones are basically the baits to lure customers. I wasted a week with them to no avails (at that time I wasn't confident enough to speak to a real estate agency but afterwards I tried anyway). And a lot of them passes apartment from this agency to another, in a kinda shared database... So you know, all the middleman's money.
Rooms around Oookayama area typically cost about 50-60,000yen, depending on the types (mansion type, with concrete structures, costs around 70,000). But September is not the high season so the price may be more reasonable than April. Anyway, you should talk directly to the real estate agency, visit the room first before making any decision. I don't have the address of my real estate agency but it's right in front of the school so you'll probably talk to them during your search anyway
. Real estate business here is a tricky thing (I can rant about this for hours) and you should do transactions directly anyway.
About the guarantor, the university will co-sign with you if you apply for a disaster insurance for 8,000yen/2 years. But not all landlords accept this type of insurance, and many real estate companies require you to pay them guarantor fees so they will be your guarantor, and it costs like half a rent, much more expensive than the university choice. My real estate agency, however, spent time to explain this university guarantor thing to my landlord, and it's not very common unless the landlord's dealt with foreign students before.
About building structure, yes, wooden ones tend to have sound problems, but that depends on the walls rather than the building structure. Some apartments have very thin wall, but some others are fine. Fire is not a big issue here since you have the insurance, and wooden ones are typically more affordable than steel structured ones. You can check when you look for an apartment about such problems anyway.