A very specific crash seems to occur when both Thaumcraft and Abyssalcraft are paired with Food Funk.
This crash only occurs when attempting to load an existing config file, even if you change absolutely nothing in the generated config. Deleting the config will make the game start properly once, but it will crash again the next time unless you keep deleting the config after every startup.

Note that this was not the case with the 1.x versions of Food Funk. The crashing started since the 2.x versions.

Forge Version: 14.23.4.2726

Used Mods:
Baubles-1.12-1.5.2.jar
Thaumcraft-1.12.2-6.1.BETA17.jar
AbyssalCraft-1.12.2-1.9.4.10.jar
Foodfunk-1.12.2-2.0.4.jar

Crash Log:
net.minecraftforge.fml.common.LoaderExceptionModCrash: Caught exception from Thaumcraft (thaumcraft)
Caused by: java.lang.NullPointerException
at com.wumple.foodfunk.capabilities.rot.RotStorage.readNBT(RotStorage.java:28)
at com.wumple.foodfunk.capabilities.rot.RotStorage.readNBT(RotStorage.java:9)
at net.minecraftforge.common.capabilities.Capability.readNBT(Capability.java:102)
at choonster.capability.SimpleCapabilityProvider.deserializeNBT(SimpleCapabilityProvider.java:119)
at net.minecraftforge.common.capabilities.CapabilityDispatcher.deserializeNBT(CapabilityDispatcher.java:135)
at net.minecraft.item.ItemStack.forgeInit(ItemStack.java:1217)
at net.minecraft.item.ItemStack.(ItemStack.java:112)
at net.minecraft.item.ItemStack.func_77946_l(ItemStack.java:396)
at thaumcraft.api.internal.CommonInternals.generateUniqueItemstackId(CommonInternals.java:45)
at thaumcraft.common.lib.crafting.ThaumcraftCraftingManager.getObjectTags(ThaumcraftCraftingManager.java:147)
at thaumcraft.common.lib.crafting.ThaumcraftCraftingManager.getObjectTags(ThaumcraftCraftingManager.java:140)
at thaumcraft.common.config.ConfigAspects.getPotionAspects(ConfigAspects.java:679)
at thaumcraft.common.config.ConfigAspects.registerItemAspects(ConfigAspects.java:514)
at thaumcraft.common.config.ConfigAspects.postInit(ConfigAspects.java:29)
at thaumcraft.proxies.CommonProxy.postInit(CommonProxy.java:82)
at thaumcraft.proxies.ClientProxy.postInit(ClientProxy.java:53)
at thaumcraft.Thaumcraft.postInit(Thaumcraft.java:54)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at net.minecraftforge.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:627)
at sun.reflect.GeneratedMethodAccessor13.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:91)
at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:150)
at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:76)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:71)
at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:116)
at com.google.common.eventbus.EventBus.post(EventBus.java:217)
at net.minecraftforge.fml.common.LoadController.sendEventToModContainer(LoadController.java:218)
at net.minecraftforge.fml.common.LoadController.propogateStateMessage(LoadController.java:196)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:91)
at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:150)
at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:76)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:71)
at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:116)
at com.google.common.eventbus.EventBus.post(EventBus.java:217)
at net.minecraftforge.fml.common.LoadController.distributeStateMessage(LoadController.java:135)
at net.minecraftforge.fml.common.Loader.initializeMods(Loader.java:749)
at net.minecraftforge.fml.client.FMLClientHandler.finishMinecraftLoading(FMLClientHandler.java:330)
at net.minecraft.client.Minecraft.func_71384_a(Minecraft.java:534)
at net.minecraft.client.Minecraft.func_99999_d(Minecraft.java:377)
at net.minecraft.client.main.Main.main(SourceFile:123)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at net.minecraft.launchwrapper.Launch.launch(Launch.java:135)
at net.minecraft.launchwrapper.Launch.main(Launch.java:28)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.multimc.onesix.OneSixLauncher.launchWithMainClass(OneSixLauncher.java:196)
at org.multimc.onesix.OneSixLauncher.launch(OneSixLauncher.java:231)
at org.multimc.EntryPoint.listen(EntryPoint.java:143)
at org.multimc.EntryPoint.main(EntryPoint.java:34)

Looks like Thaumcraft is causing something bad to happen, causing crash in capability deserialization.