I'm 90% sure I just fixed the problem for EVERYONE ON AMAZON that was affected by this.
I called again today (for the third or fourth time on this problem) and talked to a CS rep from Amazon. I explained the situation, told him what Aksys (the publisher) said on social media regarding the issue, how they were trying to reach Amazon, the whole nine yards. He understood and made sure they would be shipping the items seperately as Aksys stated, and is going to make sure it happens and of course talk to the higher ups about it as well.
Carl D. from Amazon, you may or may not be reading this, but you are a god among men. He also said "I have also been looking forward to this game sir, so I completely understand. Have you played the first two games?" I told him I had, and he said he only played the first one because he didn't have a 3DS at the time. I told him he should really play VLR before he plays this game.
So basically I may have possibly caused the domino effect to get this fixed for all Amazon customers that got screwed, and a fellow ZE fan fixed it.