Is the mind and the brain different? Sure, they are intimately connected. But is it possible that where the brain dies, the mind transcends?
So, do thoughts transcend the mind? Well, I like to think of the brain as the physical matter that exists in the skull... that slushy substance up there. The mind, on the other hand, I see as the workings of that brain, those shootings and zaps that move through, which aren't necessarily physical or permanent, nor entirely comprehensible or graspable. I see the mind as a collection of these things. Think of the leg being the physical brain, and running being the mind.
Does this make the thoughts/mind transcendent? Well, not any more than exercise is transcendent to leg. It really all boils down to whether you are willing to accept that there is an ultimate physical reality behind everything, or if you think there is something higher in the mind. Until we have enough evidence to tell us whether it is all physical or not, you can sort of understand things how you want. However, I think it's safe to notice that all discoveries we've made in the realm of science show us more and more that everything boils down to 'simple' physical interactions... if we are to call the quantum world 'simple'.
Anyway... that's just my two cents. Nice question to ponder, but I don't know what meaning it ultimately has.
Jon