I have been trying to set up Beaglebone Black using linux 3.14 kernel and Debian root file system. I have successfully compiled the kernel and device tree for BBB. Driver for invoking usb is musb. But when I boot with this kernel image and .dtb file, musb related drivers are not getting loaded. I can find nothing related to musb when I execute 'dmesg | grep musb'.
Did you install the kernel modules in the new file system?
sudo make ARCH=arm modules_install INSTALL_MOD_PATH=/media/rootfs
Replace /media/rootfs with the appropriate location in your case.