Stef is correct.
No, No, Yes
You must book with a phone agent or a city ticket office. Web fares are not eligible and there is no way to book the companion fare on-line. Fare will normally be higher than fare on the web, but with careful shopping, one can still do quite well.
Upgrade is now available only on day of travel, used to be that the ticket could be reserved and upgraded immediately. Unfortunately, that opportunity is gone and the value of the upgrade certs are drastically degraded.
You, however, can upgrade with miles at booking. Still a very good deal.