I'm not convinced there is any contribution to the quark masses from QCD instantons:
Instanton bubbles can generate a 't Hooft operator det {Qbar Q} where the det is over the flavor structure. See Terning, Ch 7. You would then need pairs of fermions to "annhiliate" into a Higgs, which then goes to its vev, leaving one pair left over. so you would have something like:
Qbar Q * (yv)^p * I
where y=yukawa coupling, v=higgs vev, p=number of pairs that are annihilated, and I is the Instanton amplitude (see, for example, Coleman's "Aspects of Symmetry", ch 7).
As you can see, even in the QCD case, I is still quite small, and so the correction is TINY relative to the tree-level Yukawa coupling. This is why I say the correction is irrelevant for SM fermions.
That being said: these effects might be there, and be important, in other contexts, such as the gaugino masses I mentioned earlier, as well as various aspects of technicolor models where there is strong coupling and chains of broken gauge groups (so there are other sources of breaking besides the Higgs). So these effects might be there in that case. But they should be irrelevant to the SM fermions themselves, as things are.
ADDED:
BTW: it is these operators that allow for violation of B and L in the early universe (both of which are anomalous, while B-L is not), and may potentially play a role in baryogenesis, for example. I just thought I'd mention that while I'm here...