I never have had Problems with GPS in OmniRom. I am back to stock since the 4.3 release (not rooted, locked BL).
With this rom I activated stamina, but the phone has a bad battary. Stock rom is more stable than OmniRom, but I also have had one random reboot with stock 4.3.
And this was short after a cold start, because sometimes I power off the phone over night.
I hope for a better stability with the next stock rom and a better battery. Maybe the new stock 9.2.A.1.199 kernel source will bring better results to CM and OmniRom.