YES! It is "BEFORE AND AFTER"! The explanations, as you got some of them...
1. Seven did not find the answer... Kes found the temporal variance in the tube, while Seven did in "YEAR OF HELL".
2. Shouldn't have been on this shuttle... future Kes was in labor while on the shuttle, something Paris warned her about.
3. Time is an enemy and a friend... time, ultimately, is the reason Kes is able to save herself and alter the ship's fate. The Krenim use time as a weapon.
4. The only time he wears it... In the future, Kim has Lt. Pips on his collar, the only time we actually see him wear them.
5. A friend is family... Kim being married fo Lynnis makes him son-in-law to Paris.
6. A different head... The Doctor in the future has hair.
7. The only time this character wears this item... Chakotay wears Captain pips for the only time.
8. Time to look back... Kes is moving backward in time. Also, Paris tells her some stories from the past... their past, but the future for us.
9. The only time we see this other character wear this... Paris wears Lt. Cmdr. pips.
10. Before it begins... Kes ends up going back to before she was born. Thankfully, that was brief.
11. One wonders how the crew encountered them... Since Kes was still on the ship in this timeline, you wonder how they encountered the Krenim to begin with, since she couldn't have sent them 9,500 light years.
12. Before a big jump... This episode happened before their first big jump in distance.
13. This episode is between seasons 1 and 3... A season 3 episode.
That seemed quite grueling. I tgought I was getting too easy with a few clues. Your turn, JP.