Hi,
Enter console mode. Option 8.
Enter :
ls -al /usr/local/sbin/ntpd
You should see :
-r-xr-xr-x 1 root wheel 692424 Oct 9 00:12 /usr/local/sbin/ntpd
This program, the time deamon, is part of a basic FreeBSD/pfSense setup. It isn't possible that it isn't there.
I really advise you to do a clean install.
True, the "Watchdog" isn't very smart neither, trying to (re) start a program that isn't there.
Not being able to check for updates could be the proof of other missing system files - or just a broken DNS setup. Don't spend more time, wipe it clean ;)