I'm surprised you were able to squeeze that much stuff in without maxing out your ROM.
I'm not the expert on this, but I can suggest a couple things...
Did you do your OTA programming after flashing? If not, try doing the *228 (option 1) and see if that helps. Not sure if it will, but it's quick and painless.
Unless you get some other advice, since you've cooked so much into your ROM, I would suggest starting over with a more bare bones ROM, test it to make sure SMS works, and then start adding programs back in to your build until you find what breaks it. Maybe someone has a better suggestion for you, but that would be mine.
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