How did you attempt to set the variables?  And from what script?  I
think you should be doing the following in ~/.vim/indent/sh.vim

let b:sh_indent_options = { 'default': value, 'continuation-line': value
}

where "value" is replaced by the values you want (number of spaces).

-- 
Vim documents non-existent indent plugin options
https://bugs.launchpad.net/bugs/479767
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