I also have had issues with PHP and nginx but on a Raspberry PI flavor board and I found this link to be helpful in getting it up and running with a MySQL database and Zabbix system monitoring a time ago.
You of course will have to adapt it to the Omega environment but it may give you some ideas of how or what you may have missed.
I have identified that the omega2p-v0.1.10-b160.bin version of the firmware contains kernel 4.4.46
On the LEDE-Project website for supported hardware, it states that the Omega2+ is supported on LEDE 17.01 which has kernel 4.4.50. https://lede-project.org/toh/start?dataflt[Brand*~]=onion
@Anthony-Kelly You might try unplugging the omega from the dock and putting a small piece of jumper wire between the receive and transmit connectors of the connector the omega sits in (just be careful to get those and not power lines - a 1k resistor would work too, and be more tolerant of mistakes).
With the wire in place whatever you type in a serial terminal should echo back, without it the echo should stop. That would test the USB-serial distinctly from the Omega 2.
Forgot about this topic for a bit. I did manage to get it working with the combination of the Omega1 tutorial and the new files from WereCatf. I had some problems compiling just the package, but I think that was my mistake.
About Lirc, I quickly abandoned it. It was much to complicated and bulky for what I needed. I ended up modifying some other code I found.