Although there are surely several methods to do this, I would opt for the method that loses the least amount of quality. And for that, I would pick
VirtualDub as my tool of choice, using the version found on this site (which has MP4 import filters pre-installed). You'll want the
HuffYUV codec. And then the AAC codec.
Get all of that here:
... and install all of it. Reboot may be required, for HuffYUV and AAC to work correctly after install.
Then you'll need to load the video into VirtualDub, and select the "resize" filter. (
Video > Filters > Add... ) You don't have to change anything, because this isn't where you'll be cropping the video.
OK. Then you'll be able to pick the
Cropping ... option. You'll want to crop the pixels here from top and bottom.
OK.
Then go to
Video > Compression and pick the HuffYUV compression. Note that this is a lossless codec, and your temporary video will be about 40GB/hour. Lossless = no quality loss due to (lack of) re-compression.
Then
File > Save as AVI and wait while the video encodes. Speed will depend entirely on the source location of the file (i.e., USB2 hard drive vs internal SATA hard drive), as well as CPU and RAM.
Then you can encode this new cropped file in your OJOSoft program, to create your properly-cropped phone videos.
Enjoy.