you have to look at the programmers guide before you remove anything of the code. The CT~ command for example changes the control prefix.
Search the internet or zebra.com site for "ZPL Programming guide".
So, leave the text file as is and then include that into your windows mobile application.
PS: zebra offers SDKs for label/receipt printers: http://www.zebra.com/gb/en/products-services/software/adapt-software.html
PS2: without a test printer you may get bad final results.