sorry to be a pain but sometime it's matters in jar my little bit.
1. It's the IRS that aligns not the FMS. Also more relivently i'm almost sure (having done jar's about 3 years ago) the jar ans to that is in NAV mode this is the normal way to do it in operations unless you are short on time.
2. As above can't do better than that.
3. As for wind vector not sure to be honest nothing in the boeing ops manual. But as far as i'm aware it's is driven by the IRS therefore unless you lose both of them i't should be there hopefully someone else can correct me if wrong. Only time it blanks is if the velocity drops below 4kts, if you havent experienced more than 6kts yet or your TAS is less than 101kts.