The Interview will take place over the skype video chat, once all the initial setup for smooth conduction of interview are in place.

 
You will have a contract with the company directly. If you pass the interview, you will get an acceptance letter cum Appointment letter.

 
There are two ways to apply for a visa: 
(1) The visa applicant him/her goes directly to the Japanese Embassy / Consulate General, with a Letter of Proxy from his invitor to Japan, and gaurantor letter, to apply for the COE from Japanese Embassy / Consulate General at his/ her place.
(2) the visa applicant uses an accredited travel agent approved by the Japanese Embassy / Consulate General. However, depending on the circumstances in your country or region, there are cases that the documents should only be submitted by the applicant him/herself going to the Japanese Embassy/Consulate, or through an accredited travel agent. 
Check with the embassy or consulate for which plan you would want to apply before making the application.

 
Yes, the company shall help you with suggestions on where you can find your house. Provide you with necessary proof of employement and salary, at the time of registering yourself at rental providers.