[otrs] OTRS Win32 to OTRS Linux Migration - What are the issues?

I am currently using OTRS on Win32 but am going to migrate to Linux. Are there any major 'gotchas' to be aware of? I have modified over a dozen different files in the Win32 source. Can I create diff patches and apply them directly to Linux source or will I have problems there? Currently I both send and receive mail from an exchange server. I send out directly via the SMTP modules. I get mail via a POP3 account and a cron that runs every minute. Anything different there or can I continue to use this same process? Thanks, Tyler Hepworth