‘Dumb’ search-and-replaces (and I mean that as a comment on the code, not on you!) always strike fear in my heart; if we can't even parse such a rigid language as XML with regexes (which we can't, right? Or at least no sane person would?), how can we expect correctly to parse the rich grammar of a programming language? I always think of clbuttic.
If this were my job, the first thing I'd do would be to look at some means of getting at the internal, not textual, representation of a PHP program. The first result for PHP + AST is php-ast; I'm not sure if it does what you want, but you might be able to fold, spindle, and mutilate it, or else just look further down in the results.