My experience with shareholder's certs:

Shelf life: I just sold 7 (5 ANA and 2 JAL) to a ticket store in Kobe last month for something like 47,000 yen as they had over 6 months of validity. This was a very good price.
I gave away a few in February (expiring end of March) as the ticket stores only offered 1,000 yen each.

Connection flights: I was told one certs for each leg

Tokuwari vs certs: For saturated markets like Tokyo-Osaka, the Tokuwari fares-limited seating one day advance puchase- are pretty closely priced if your schedule is firm.

Prices to buy the certs at Chiketto Shops (ticket shops): You'd think are also depended on shelf life. But I have been never been quoted less than 5,000yen :<
Lots of Chikketto shops are located close to most bigger stations, sells and buys prepaid phone cards, train tickets, etc, etc and are perfectly legal.