Using ffmpeg with Windows and AWS EC2 for encoding videos

I currently an attempting to find a solution for a video project that I'm working on. I'm trying to convert a .wmv file ~20 minutes long and around 1 to 2GB in size to three different file formats, those of which being iPhone, mp4, and another wmv with specific brightness and contrast settings with a watermark in the bottom right of the newly encoded video. I currently have a Windows desktop machine with an i7 860 processor and 8GB of RAM that I'm going to be doing video encoding on with, and am wanting to use ffmpeg to see if I can increase the turnaround time of conversions considering the current program I'm using is taking up to 2 hours to convert just the mp4 and wmv formats with those few settings. Additionally, considering I'm not around my desktop all the time, I'd like to have the flexibility of having the needed commands available to make this work in an Amazon EC2 Linux instance with ffmpeg on one of their instances. This is a fairly low budget project, so please bid accordingly.