For the etc/init.d/gps: not found issue: there was a typo in the Omega2 LTE Guide, it should be /etc/init.d/ugps
Our mistake! We've fixed the typo in the guide.
And for the original lack of GPS positioning data, it sounds like it's not able to get a lock on enough satellites. The route you were pursuing - reading the raw NMEA strings - is definitely the best first step in debugging this and should provide you some more details.
What kind of antennas did you test? Can you share a photo of your setup?