After Effects Issue uploading to Youtube - Screen Resolution

Hi All
I've been struggling lately trying to get my set of youtube videos to appear at the proper resolution and ideally fullscreen without the black bars at the side.
Youtubes recommended sizes:
1080p: 1920x1080
720p: 1280x720
480p: 854x480
360p: 640x360
240p: 426x240
My original videos are recorded in 1280x1024 which is what my screen resolution is set to, when I drop these videos into AE i set the comp size to 1280x1024 and i get a normal correct sized video. However when i render it out and upload it to the site I am given black bars down the side of the video and it does not appear full screen. (The quality is not great either if you do go fullscreen mode in the player - but the bars remain)
Now youtube state this is fine and works ok but as a personal preference i'd just like the video to fit the player.
but your not rendering at the recommended settings I hear you say; well, when I change the comp setting to 1280x720 i lose the top of my video and I am stuck as to how to fix it. Is the issue i'm having to do with the original video size, should i change resolution and record at 1280x720 (i dont have a widescreen) or is there a way around this in AE? I hope its not as easy as just scaling the video down in AE and forcing it to fit, something just feels wrong when I do that.
i would apprecaite any help! I really would.
Simon
(Additional - Recorded at 30FPS and Output in H.284

You should be using the YouTube HD preset in the Adobe Media Encoder and your comps should be either standard HD 1080p or 720p. No matter what you upload to YouTube they will process the footage and set up the other resolution options.
The important thing here is that youTube videos are either 16X9 or 4X3. Anything not at that picture aspect will end up with black borders at the top or on the sides. There is absolutely no way to override this. It cannot be done. The only way you can provide non standard video frame sizes to the public over the Internet is to use a codec that supports odd frame sizes and load it on your own server. All streaming services have standards and they are the same frame size.
If you want to see your entire screen capture then you should either set your screen resolution to 1920 X 1080 and capture that or simply scale your screen capture footage or project so that it will fit into a standard HD comp.
Saving a few KB in file size is not what you are looking for. The best picture and sound quality you can get in a streaming format is. That can only be achieved using the Adobe Media Encoder. The YouTube Presets are already optomized for the best you can get with this software for this delivery format. There is no need to re-invent anything. Just use the presets.

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