#Bash + GNU utilities, 204
fold -$1|sed 2~2{s/.\\+/printf\ %$1's "`echo "&"|rev`"/e y/'`printf %s {A..Z} {a..z}`"&_?!\"'.,/∀qƆpƎℲפHIſʞ˥WNOԀQɹS┴∩ΛMX⅄Zɐqɔpǝɟƃɥᴉɾʞlɯuodbɹsʇnʌʍxʎz⅋‾¿¡„,˙'/ }" 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 $ $ echo "The quick brown fox jumps over the lazy dog." | ./boustrophedon.sh 30 The quick brown fox jumps over ˙ƃop ʎzɐl ǝɥʇ $ ###Explanation
fold -Nsplits the input into lines of length N.- The rest of the processing is done by sed, line-by-line:
2~2matches every other line, starting at line 2s/.+/printf %'N's "`echo "&"|rev`"/euses GNU Sed's exec feature to call a shell to reverse the line and left-pad it with up to N spacesy/ABC.../∀qƆ.../transform characters
Note ABC... is generated using a bash expansion and printf. Also some fancy quoting for all the different characters.