You can put togther a composite period for company B by including the 4th quarter from the previous fiscal year and removing the 4th quarter from fiscal 2012. Since company usually don’t report 4th quarter data seperately you will need to calculate the 4th quarters by removing the 3rd quarter year-to-date period from the full fiscal year.
You can define a chart of accounts as group chart of accounts and do consolidation. and at group level you can give Jan to Dec fiscal year to generate financial statements.