Aw crap, I'm sorry to hear that you're having issues man, I was hoping that this particular mani might be ok.
I sold udontknowjack this manifold, so obviously I went with option A... But originally my plan was to run the manifold with a FMIC, which ought to take care of things. However, I knew it was going to be ages before I installed one, and it had already been ages I'd had the mani sitting around, that's why I sold it.
I think the idea with that tube, rather than it being able to stand up to the heat, is that it's longer than it needs to be. This allows you to install some ~1/4" nylon bushings/spacers below that corner of the TMIC (you'd need a longer bolt too). That way the TMIC is lifted up higher than it normally sits, which gives clearance between it and the manifold runner.
So I'd say, create option C first, which is to raise the TMIC. I'm sure Ken can help you with that because he feels bad there're issues with his part. Also there are some threads related to fixes, linked in www. mazda speed forums. org/forum/mazdaspeed-3-6-sale-trade/9441-fs-brand-new-ms3-manifold.html#post58552
Good luck!