Some Questions

Hi! My husband and I will be visiting Japan this April and would like to stay for as long as possible, but we don't know if more than one month is in our budget. We have found a place to stay for 70000 yen/month in Tama Plaza (I think it's in Kawasaki?). We don't eat often due to a health-related diet, and will be buying food to cook ourselves (we've agreed to eat out only twice). We would like to explore Tokyo (Harajuku, Shibuya, shrines and temples, etc) and also the Ghibli Museum. Before we leave Japan, we want to get a JR Pass (7 days) and visit Miyajima, Hiroshima's Peace Park, and one other place (either Kyoto or Mt. Koya, but we aren't sure how we'll get to Mt. Koya since the JR Pass doesn't go there). Anyway, if we only stay at the very least expensive places, how much do you think our total trip will cost us for the 1 month in Tokyo/1 week elsewhere?

I'm also wondering about Pasmo and Suica. Can Suica only be used on JR lines? And how do you apply for a Pasmo Pass? And is it very difficult to get around Hiroshima and Kyoto with a JR Pass?
Also, on the JR website, what does this statement mean: Note also that passengers using JR trains on non-JR lines must pay additional fares and charges for sections traveled on such lines.

How can you be on a JR train on a non-JR line? Sorry I'm so ignorant about this..

Sorry, this probably all sounds confusing. Actually, I'm a little terrified that I might get utterly lost in Japan. I've been to Tokyo, Kyoto, and Hiroshima on foreign exchange before, but I always had my host family to take me everywhere.

Thanks everyone!

but we aren't sure how we'll get to Mt. Koya since the JR Pass doesn't go there

It is explained here:
http://www.japan-guide.com/e/e4904.html

Anyway, if we only stay at the very least expensive places, how much do you think our total trip will cost us for the 1 month in Tokyo/1 week elsewhere?

I would budget around 150,000 to 200,000 yen for the 1-week trip to Western Japan, including accommodation, transportation, meals and sightseeing on a very cost conscious budget.

For the other three weeks, I would budget around 150,000 to 200,000 yen, including rent, food, household, transportation and sightseeing.

For a total of 300,000 to 400,000 yen for the whole stay, not including the flight to Japan.

I'm also wondering about Pasmo and Suica. Can Suica only be used on JR lines?

No. It can also be used on non-JR transportation in the greater Tokyo area:
http://www.japan-guide.com/e/e2359_002.html

And how do you apply for a Pasmo Pass?

Pasmo cards can be purchased at vending machines. But if you get a Suica card, there is no need for a Pasmo card. Commuter passes can be purchased at ticket counters of railway stations.

And is it very difficult to get around Hiroshima and Kyoto with a JR Pass?

No. Inside the cities of Kyoto and Hiroshima non-JR buses, trams, subways and trains are more useful.

Also, on the JR website, what does this statement mean: Note also that passengers using JR trains on non-JR lines must pay additional fares and charges for sections traveled on such lines.

It is explained in more details here:
http://www.japan-guide.com/e/e2368.html