bbb filesystem export

Hi guys,

Currently I have have developed a project on a of the off-the-shelf beaglebone image using the RobertCNelson/netinstall solution and the output is a flasher sdcard image.
Now I have figure out that there is no control over the u-boot, device tree, kernel source.

My first question is on how could I backup the up and running bbb filesystem then add/import/use it to a new build from scratch kernel?

Secondly how could I edit the RobertCNelson/netinstall image, and what kind of change can I make?