The boots are still quite pliable and soft so I don't think it was a storage issue. I also don't believe the Honda stopped making these either so they should actually be new and not NOS. Well I started to think about the problem and I've come to this conclusion.
I am not running a stock airbox, I run with these airboxes from Steel Dragon Performance. I got to thinking that since a stock airbox actually bolts to the frame in the rear, the whole carb rack is supported in the front by the boots and the rear by the box, the carbs are essentially rubbermounted on both ends. Since I'm running non stock boxes, the whole weight of the carb rack is on the front boots and clamps. It's kind of strange that it would just tear like that completely through like it did, but those Steel Dragon Performance are made with beefy aluminum so they do add a lot of weight to the whole setup. Not to mention going over bumps and whatever else while riding is causing the carb rack to flex on the boots right at the clamps. It's only a $70 mistake on my part I guess and ultimately I'm glad it's now when I'm home and not out on a trip or something.
I think most people that are running with pods, stacks, or airboxes like mine with stacks built into them don't support the rear section of the carbs and I haven't ever read about this happening to anyone else. I thought I would just share my experience with everyone and show the solution I came up with. It's not elegant, but no one is going to see it either. I think supporting them back here with some safety wire in this configuration should do the trick.