How to change the boot kernel of a usb live w/ persistent running Kali

First, the issue that I'm having is being unable to run VirtualBox on Kali 2.0. I set up a usb live with persistence running Kali 2.0, which at the time had the 4.6.0-kali1-amd64 kernel. I have since updated/upgraded/dist-upgraded etc with all of the recommended sources. As a part of this, the new headers/kernels that have been installed are 4.9.0-kali4-amd64. However, even after boot, the kernel is 4.6.0, as confirmed by uname -r and the error thrown by vbox. I know normally grub needs to be config'd, though there is no grub bootloader in the usb live boot. The error thrown by virtualbox says that no suitable driver was found for the 4.6.0 kernel, and also that the system is not set up to dynamically create drivers (though I believe that this is due to the fact that it is making the driver for the 4.9.0, but this is not the running kernel).