Do you have suggestions for low percentage of retrieval of protein from the IgG column for the TAP-tagged yeast strains?

After TEV cleavage, try a higher salt concentration in your elution buffer to help dissociate the protein from the column. Keep in mind that high salt, acidic pH elution buffers may also elute some of the zz domain of Protein A. This can cause interference with subsequent use of the anti-TAP antibody