What Is So Rare… – answers
1) The second of the same name. Junior (oomis1105, ronrsr, anon for this)
2) Twain’s villainous Native American. Injun Joe (YW Moderator-80, oomis1105 [this answer also served as a clue for #9])
3) A type of boat. Junk (ronrsr)
4) An overgrown tropical area. Jungle (smartcookie, oomis1105)
5) A promotional trip. Junket (oomis1105, ronrsr, anon for this)
6) A point in time. Juncture (anon for this [this was a tough one, easily confused with junction])
7) A type of evergreen. Juniper (oomis1105, ronrsr, anon for this)
8) An assistant. Adjunct (oomis1105, anon for this)
9) A key automobile component. Enjun (YW Moderator-80 )