You didn't mention if you are using DBI. If you are, your transition will be eased, but not eliminated. You will still face the problem of differences in the SQL dialects between the two. If you are using relatively few MySQL specific features, you should be ok. I would recommend using DBD::ODBC for MSSQL. You can also use DBD::Sybase but as MSSQL diverges further from its Sybase origins (which MS has announced it will do), that option will become less viable.
Comment on Re: CGI MySQL script to ASP(perlscript) MSSQL
Re: DBD::Sybase and MS-SQL becoming less viable...
As DBD::Sybase requires FreeTDS to work with MS-SQL the real issue is how well the FreeTDS folks can track the changes that MS introduce and map them back to the Client Library API that DBD::Sybase uses.
Thanks for clarifying. I hope no one misinterpreted my remark as in any way denigrating the excellent DBD::Sybase. If someone interpreted it as denigrating MS-SQL, well, I can live with that :-).