Upgrade from 10.3 to 11.0 broke the system

Hello, I'm fairly new to the world of BSD but decided to give FreeBSD a try. So far I love the system but unfortunately I think I messed up with the system upgrade, because freebsd-version and uname are giving different kernel versions:

# freebsd-version -k

# uname -a
FreeBSD <hostname> 11.0-RELEASE-p2 FreeBSD 11.0-RELEASE-p2 #0: Mon Oct 24 06:55:27 UTC 2016 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64

What I believe I did is that I forgot to do:

# freebsd-update fetch
# freebsd-update install

before attempting:

# freebsd-update upgrade -r 11.0-RELEASE
# freebsd-update install

Most of the remote services I installed still work, including sshd. However some files are missing due to the system being in this inconsistent state.

Despite this, I tried going on with freebsd-update upgrade like the guide said but here's the output:

# freebsd-update upgrade
src component not installed, skipped
Cannot identify running kernel

Now the question, is there a way to recover my system from this state?

Sorry for the long intro, I thought it was better to give as much information as possible.
The first install after the upgrade only upgrades the kernel. You need to run freebsd-update install a total of three times, as the instructions clearly state.

freebsd-update upgrade -r 11.0-RELEASE
freebsd-update install
freebsd-update install
(reinstall all ports/packages)
freebsd-update install
The problem is that I am not able proceed due to the 'Cannot identify running kernel' error I get from freebsd-update after the first reboot.

Edit: I have found a somewhat strange thing about my kernel:

# sysctl kern.bootfile
kern.bootfile: /boot/kernel/INS@E1RV

The script in freebsd-update checks if kern.bootfile is a directory, but that path leads to a file, so it fails to proceed.