I would only make suggestions towards hotels. I agree with [MENTION=101566]kaka[/MENTION] try the Toyoko-Inn chain. Low priced, especially if you become a member. They are all over Japan, close to rail stations, clean, safe, modern, have friendly staffs, have breakfasts, many have or are next to mini marts, almost all have self service laundries. All of these features will help extend the couples budget.
End of unpaid endorsement.