No, I am not using the standalone omnifactory mod.
As for the last error message:
Spoiler
"16507 [Thread-5] ERROR com.fs.starfarer.combat.D - java.lang.NoClassDefFoundError: org/lazywizard/omnifac/OmniFacSettings
java.lang.NoClassDefFoundError: org/lazywizard/omnifac/OmniFacSettings
at data.scripts.ExerelinModPlugin.onApplicationLoad(ExerelinModPlugin.java:81)
at com.fs.starfarer.loading.G.super(Unknown Source)
at com.fs.oOOO.oOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO.Ò00000(Unknown Source)
at com.fs.starfarer.combat.D.o00000(Unknown Source)
at com.fs.starfarer.StarfarerLauncher$2.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: org.lazywizard.omnifac.OmniFacSettings
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 6 more"