This message was posted on behalf of Intel Corporation
I've an idea that might be able to help you but you will have to build your own image and strip it from all the packages that are not required in your project. If you do so, you will be able to build an image that is shorter in size and you'll be able to inset it into the Edison's drive. If you would like to learn how to build a Yocto image and how to modify it, I'd suggest you to read the following documents:
Once you have created an image that both fits your needs and is able to fit in Edison's drive, you will have to create a similar method of updating to "configure_edison --upgrade". I mean, as you mentioned, there was a method of updating the image that was similar to an over the air (OTA) update. Since you would like to update the Edison through a remote connection I'd suggest you to read this section of "configure_edison". You can find the source file of configure_edison in /usr/bin/configure_edison.
I hope this information helps.