1-wget approx. 5000 rar files total from 2 different servers
Depending on what you are doing here with wget (FTP, HTTP, HTTPS) you can use LWP or Net::FTP to avoid running 5000 instances (exec's) of wget.
2-unrar the archives into approx. 16000 files of 4 different types
This can't really be made faster with perl.
3-move/rename the files into different directories based on file type
Avoid this step altogether (do the final placement while doing step 5).
4-run one group of files through a series of sed filters producing a modified set of files
You can run this through your script without invoking sed so many times. Perl has built in functionality that can do this task on one process.
5-copy all files (now approx. 20000) into a matching directory structure on a Windows box via smbclient
Copy (to the renamed new directory target) the files to the structure that you need o the Windows server at this time. Do not need to move stuff around in step 3 at all.