Jason,
For some reason the aspect ratio was changed, never had that problem but I don't use .WMV or .AVI. For Youtube you want to work with H.264 encoding in an .MP4 container file. .MOV is also OK if your encoding from Quicktime on a Mac. The X.264 encoder is best, and is found in the free and excellent Handbrake and MPEG Streamclip apps. Keep the settings simple for Youtube uploads, as the files are re-encoded anyway. Work with a constant bitrate of 5 to 8MBps for a 720p upload, any more is a waste and can cause problems with the YouTube encoder. I have values at home I can post later, but there are basic settings listed all over the net and in YouTube help. YouTube does look like crap compared to higher bitrate and profile encodes on your own machine or host.