#Bash + GNU utilities, 204

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 fold -$1|sed 2~2{s/.\\+/printf\ %$1's "`echo "&"|rev`"/e
 y/'`printf %s {A..Z} {a..z}`"&_?!\"'.,/∀qƆpƎℲפHIſʞ˥WNOԀQɹS┴∩ΛMX⅄Zɐqɔpǝɟƃɥᴉɾʞlɯuodbɹsʇnʌʍxʎz⅋‾¿¡„,˙'/
 }"

N is given on the command line and S is given via STDIN:

 $ echo "The quick brown fox jumps over the lazy dog." | ./boustrophedon.sh 30
 The quick brown fox jumps over
 ˙ƃop ʎzɐl ǝɥʇ 
 $ 

###Explanation

- `fold -N` splits the input into lines of length N.
- The rest of the processing is done by sed, line-by-line:
 - `2~2` matches every other line, starting at line 2
 - ``s/.+/printf %'N's "`echo "&"|rev`"/e`` uses GNU Sed's exec feature to call a shell to reverse the line and left-pad it with up to N spaces
 - `y/ABC.../∀qƆ.../` transform characters

Note `ABC...` is generated using a bash expansion and printf. Also some fancy quoting for all the different characters.