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You have unnecessary spaces in the strings defining your recipe. For it to fit in a 2x2 square, define it using 2 strings of 2 characters each, rather than 3 of 3.

If you expect the list to always contain elements, step through the code where you populate the list using your debugger, to find out why it isn't being filled like you expect. If you just want to prevent a crash for cases where the list has no elements, use ArrayList#isEmpty() to check.

Ah, that makes sense. That warning is misleading, then

(https://docs.oracle.com/javase/specs/jvms/se8/html/jvms-5.html#jvms-5.4.1) This is probably a reference that you haven't read, but just googling for "java.lang.VerifyError" yields similar results. What this error means is that some class was malformed or otherwise screwed up at runtime. This is usually the product of meddling with coremods and ASM and stuff. So this is probably caused by Optifine, the only 3rd party coremod installed. You can also, higher up in the log, see that Optifine printed an IOException it caught, which, almost certainly, led up to the VerifyError. You should do that. (PS for smarter ppl than me: I don't get why optifine is not listed in the core mod list even though its transformer is clearly being loaded.)

That's precisely what it is. A top half and a bottom half.

Surprise. http://minecraft.gamepedia.com/Flower#Data_values There's three.

You might want to take a look at this: https://github.com/Draco18s/ReasonableRealism/blob/master/src/main/java/com/draco18s/hardlib/api/internal/CommonContainer.java#L23-L33