My problem is when I use the animated gif the background it is no longer transparent and the background is instead white.
Correct. As a conmpositing program, AE requires proper Alpah transparency, not palette-based transparency. File must be converted to an image sequence with Alpha channel.
Next the animated gif is about a 2 second loop, it won't let me drag the bars to extend the time to 10 seconds. How do I loop it for 10 seconds?
Footage interpretation --> Loops
1) For the text effect 'numbers' (which I used for the countdown effect) it always renders really shaky and bouncy when i preview it. Is that normal?
Yes, it's normal if you are using a non-monospaced font. Use a suitable font.
2) It has the time as 00:00:00:00 (type: timecode 30). How do I make so it only shows 00:00 ?
Use multiple layers and effects and mask them out.
XnView, ACDSee, Irfanview or any image viewer/ converter via their File --> Save as... options or batch processing. If you have Photoshop, you can do this by adding the GIF as a video layer and exporting to an image sequence (TIF, PSD etc.).
I imported the gif to photoshop and saved it as a psd (it doesn't let me click on a checkbox for alpha channels, is that ok?)
Next how do i exactly get after effects to see it is an animation even though it is a psd? I thought it would be simple and just put import as footage, but then it asks me layer options and all that other stuff. I tried playing around with a few options, but it just seems to come in as a still image.