I don't know where you live, but my Barnes and Noble store has people who are truly experts on Nook Color and Nook Tablet - I'd take it in to the store - mayber they'll exchange it for another unit.
[...] I can charge the Nook to 100% and unplug it and read for a while. When I'm done I normally put it into sleep mode which, before the update, never gave me any problems. It used to be at like 95% from reading and put it to sleep and when I come back like 7 hours later it MIGHT be down to 94% or still at 95% but now when I put it down at 95% and come back x amount of time later the Nook is shut off and completely powered down/low battery and I have to recharge it in order to use it again.
That sounds like one of two things: Either your battery is defective, or something is hanging and keeping the unit awake/waking it up and eating up battery. Do you notice if the screen is already on when you look at it in the morning?
You could try a rest on the device to clear up all the software settings. While you haven't added anything unusual, there could be a configuration issue that's keeping the unit from entering deep sleep (battery saving) mode when the screen is off. If that fails to fix it, I'd take it by a store and let them look at it.