What version of AE do you have. Earlier versions had problems with MP4 video. It's always best to transcode highly compressed sources before you start manipulating video.
Somewhere in that template there's place holder video or a place holder layer. You must find the original footage layer not the pre-comp, not the nested comp. Once there all you have to do is select that place holder layer in the timeline then select your new video in the Project Panel and hold down the Alt/Option key and drag to the timeline. The footage will be replaced.
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What Rick said - older versions of AE may not at all be able to handle the source formats you mentioned and even in CS5.5 not every source is guaranteed to work. There are just too many flavors of MPEG 4 and e.g. many photo cameras that also record video produce out-of-spec files that AE has no handle on. Likewise, specific sub-sets of MP3 may contain DRM protection, multiple channels and whatnot, all of which may also not go down well with AE...
Well it worked. I encoded the file to MP4 using adobe media encoder and that worked. I previously used handbrake to encode to MP4.
Thank you all