Yea ... I'm in the same boat here. My PC is Windows and my Server is a remote Linux Server.
Just do as jtp10181 suggested.
You can download the Linux files and unpack/save them to your Windows HD, then you just need to upload to your Linux server via FTP. The files work fine, it dosen't corrupt them by having them on your Windows PC.
If you need to compile plugins then just compile on your PC and upload, no problems.
NOTE: I do have a habit of saving any config files in UNIX format though, just incase. (LF / CR and LF differences between the operating systems.)
@ jtp10181 ... It's easy when you know how