Kant argues for a separation between the noumenal world and the phenomenal world, for good reason. Kant does not, however, seem to believe the mind is noumenal. If we operate on a brain and we remove a segment which permits the smell of roses, completely, so the thought of the smell of roses could no longer be perceived, how would Kant say this occurred? Would he describe this as a removal of a priori structures permitting the smell of roses?
On the contrary, Kant does make a phenomenal-noumenal distinction with respect to the mind. In the following, for example, he speaks of us knowing ourselves only as we appear to ourselves:
"We have now arrived at the proper place for explaining the paradox which must have struck every one in our exposition of the internal sense, namely—how this sense represents us to our own consciousness, only as we appear to ourselves, not as we are in ourselves, because, to wit, we intuit ourselves only as we are inwardly affected." (Critique of Pure Reason, B151)
Elsewhere, he says the following:
"[A]lthough my own existence is certainly not mere phenomenon (much less mere illusion), the determination of my existence can only take place conformably to the form of the internal sense, according to the particular mode in which the manifold which I conjoin is given in internal intuition, and I have therefore no knowledge of myself as I am, but merely as I appear to myself. The consciousness of self is thus very far from a knowledge of self, in which I do not use the categories, whereby I cogitate an object, by means of the conjunction of the manifold in one apperception." (Critique of Pure Reason, B157)
As far as the smell of roses, Kant did, in fact, refer to the conditions of sensibility as a priori as you said:
"For that objects of sensuous intuition must correspond to the formal conditions of sensibility existing a priori in the mind is quite evident, from the fact that without these they could not be objects for us;" (Critique of Pure Reason, A89/B122)
If I'm understanding your question correctly, you seem to be associating the idea of the brain with the noumena. However our knowledge of the brain is only by means of phenomenal evidence. Furthermore, anything which may affect the noumena shouldn't be confused with the noumena itself. Removing a part of the brain has effects on how we perceive the world, but we can only investigate the causal chain of physiology phenomenally and cannot assume that there are no unseen factors at work beyond our perception.