I am getting large numbers of these:
[16:06:59] [Client thread/ERROR] [BiomeTweaker]: Failed to retrieve inserted fields!
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: java.lang.NullPointerException
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at me.superckl.biometweaker.util.BiomeHelper.fillJsonObject(BiomeHelper.java:41)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at me.superckl.biometweaker.BiomeTweaker.onLoadComplete(BiomeTweaker.java:73)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.lang.reflect.Method.invoke(Method.java:606)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at cpw.mods.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:513)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.lang.reflect.Method.invoke(Method.java:606)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at com.google.common.eventbus.EventSubscriber.handleEvent(EventSubscriber.java:74)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at com.google.common.eventbus.SynchronizedEventSubscriber.handleEvent(SynchronizedEventSubscriber.java:47)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at com.google.common.eventbus.EventBus.dispatch(EventBus.java:322)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:304)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at com.google.common.eventbus.EventBus.post(EventBus.java:275)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at cpw.mods.fml.common.LoadController.sendEventToModContainer(LoadController.java:208)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:187)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[16:06:59] [Client thread/INFO] [STDERR]: [java.lang.Throwable$WrappedPrintStream:println:748]: at java.lang.reflect.Method.invoke(Method.java:606)
...

This happens during early startup, and was caused by
allBiomes.set("liquidFillerBlock", minecraft:air)

Ahh ...

For what it's worth, it worked without the quotes. I don't know if that's because it just wound up with "null", that happens to be air or not. Lets see if the error messages go away

Yep, errors are gone. Thank you.

Yeah, no problem.

The parser would usually catch such a mistake, but it can't for the 'set' command since the second argument depends on the first, e.g. 'grassColor' takes an integer, while 'fillerBlock' requires a String.

You need to wrap the block name in quotes:

allBiomes.set("liquidFillerBlock", "minecraft:air")