clarification on visiting hikone city

Hi I am wanting to go from kyoto to hikone city to see castle and lake biwa.

From hyperdia it says when I put in kyoto sta to hikone sta;
Kyoto bullet train hikari transfer maibara jr special rapid service hikone station.

When I put in kyoto station to minamihikone it says kyoto station then jr biwako line arrive minamihikone (no transfer)

What is the difference between hikone station and minamihikone? Or are they the same?
Should I assume I can use my jr pass on jr biwako line?

Thank you for the help!

Kyoto bullet train hikari transfer maibara jr special rapid service hikone station.

This is just one (fast but expensive) option. Another (cheaper, slower but direct) option is to take the direct special rapid train. I am sure it is listed as result 2 or 3 by Hyperdia. If you don't want to see the shinkansen in your Hyperdia searches, un-check "shinkansen" in the search details.

What is the difference between hikone station and minamihikone?

Two different stations. See map:
http://goo.gl/maps/OE3z0

Or are they the same?

No.

Should I assume I can use my jr pass on jr biwako line?

Yes, the Japan Rail Pass is valid on the JR Biwako Line. But if you have a Japan Rail Pass, I would consider taking the shinkansen option. It can be considerable faster.

Thanks! Yes, I just found the direct jr special rapid service via hyperdia that is direct from kyoto to hikone.

Two questions;
1. in nagoya city can one use the suica or plasmo card to jump on and off subway/bus? Or is there a card I could use in both nagoya and kyoto to do this?

2. I would like to travel back from hiroshima to tokyo on sat sept 20th around 1500, but I cant seem to find a route that I can use 100% using my jr rail pass. Ive checked on hyperdia. Any advice would be appreciated.

Another option from hiroshima is to return to shinagawa station instead of tokyo station.

1. in nagoya city can one use the suica or plasmo card to jump on and off subway/bus?

Yes. Alternatively you can use Manaca, Icoca and many more. See more details here:
http://www.japan-guide.com/e/e2359_003.html

Or is there a card I could use in both nagoya and kyoto to do this?

Suica, Pasmo, Manaca, Icoca, etc. are also valid on the trains and subways in Kyoto, but until later next year, the Kyoto buses cannot be used with these cards. It is scheduled that the cards will become valid on Kyoto buses by spring 2015.

I would like to travel back from hiroshima to tokyo on sat sept 20th around 1500, but I cant seem to find a route that I can use 100% using my jr rail pass.

If you use Sakura and Hikari trains along the Tokaido/Sanyo Shinkansen with a transfer at ShinOsaka, the trip will be fully covered. You not allowed to use the Nozomi trains, though. See more details below:
http://www.japan-guide.com/e/e3404.html

Ive checked on hyperdia.

In order to get connections covered by the Japan Rail Pass on Hyperdia, you have to un-check the NOZOMI option under "Search Details".

Thank you uji, so if I purchase a icoca card in nara for the bus, I will be able to also use it in okayama, miyajima, himeji, and hiroshima? Can I then after im done with it turn it back in at hiroshima station to get refund/balence on the card? Can one card be used for two people or should each have their own?

so if I purchase a icoca card in nara for the bus, I will be able to also use it in okayama, miyajima, himeji, and hiroshima?

It does not matter where you purchase the Icoca card. But the Icoca card, indeed, has the advantage over other IC cards that it can be used on buses in Nara and buses/trams in Okayama, Himeji and Hiroshima as well as on the JR ferry to Miyajima.

In Nara, the Icoca card is probably only available for purchase at JR Nara Station.

Can I then after im done with it turn it back in at hiroshima station to get refund/balence on the card?

Yes.

Can one card be used for two people or should each have their own?

Each traveler needs to have its own card.