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# Python, 222 bytes
(202 characters)

<!-- language: lang-python -->

 import re
 def f(s):y=[w[0]in'ˈˌ'and w or' '+w for w in re.split('([ˈˌ]?[bdfhjklmnprstvwzðŋɡʃʒθ]?[aeiouæɑɔəɛɜɪʊʌː]*)',s)[1::2]];return[[x[i-1:i]or' 'for x in y]for i in range(max(len(w)for w in y),0,-1)]

Returns an array of unicode characters with an array for each row (containing single spaces for each space required)

Not sure where one can get decent output online yet (and I haven't even got the tools to test it properly here either). 
I have loaded a version to [**ideone**][1] that just uses English consonants and vowels with `,` and `.` as stress marks, where I have fudged the test cases to conform.


 [1]: http://ideone.com/O2rr7v

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