Although I haven't created my own custom image for the Edison yet, the Intel Edison Board Support Package that goes over creating a custom image does show that one can choose a 64 bit kernel in the section Customizing the Linux Kernel. That BSP document can be found here: Intel® Edison BSP User Guide
The process of customizing your Edison image (as per the BSP) outlines how to add and remove packages for the image as well.
There is a Debian Wheezy (stable) based ubilinux image that you can find discussed here. https://communities.intel.com/message/256964#256964