1.  kingdom order class -> phylum             (taxonomy)
2.  bogart bacall lennon -> ono               (Humphrey & Lauren, John & Yoko)
3.  men wheat boys -> chaff                   (separate the ... from the ...)
4.  emit time mite -> item                    (anagrams)
5.  blitzen donder vixen comet -> cupid       (original reindeer names)
6.  lambda kappa theta eta -> iota            (Greek letters)
7.  kill steal covet bear -> commit           ("no-no" verbs)
8.  joseph benito winston franklin -> adolf   (Western leaders during WW II)
9.  bobby jan greg marcia cindy -> peter      (Brady kids)
10. handle king sauce pan crab -> apple       (king-crab-apple-sauce-pan-handle)
11. deer cheep eye neigh bye -> cell (or cel) (homophones of antonyms)
12. it about all read extra -> extra          (cliche)

Final: mi fa do ti re la -> so (or sol)       (notes of scale)

It's been pointed out to me that "hie" and "high" (homophones of "hi",
which is the opposite of "bye", which is a homophone of "by") are also
possible answers to number 11.  Ah well.  My apologies if this tripped
you up.

By the way, about those reindeer: If you want to know why I used "Donder"
rather than "Donner", check out http://www.cknow.com/info/donder.html .