> That being said, is there a better way other than manually  
> going through my XML file and changing those characters to their  
> correct entity code

If you are still not convinced that the need for entity refernces is
spurious, then the alternatives are to use d-o-e (if your xslt processor
supports that) or if you are using xslt2 to use character maps .
Character maps that will write out mathematical characters using
MathML/ISO entity references may be found here
http://www.w3.org/2003/entities/iso9573-2003doc/overview.html
(I generate those despite arguing that they are not needed:-)

david