In the antibody-oligo kit, I wonder if, after the purification process (part B and C in the user manual), all of the unconjugated DNA oligo and antibody should be removed from the system? if so, can we use the total antibody concentration as the value for the coupling product?

The protocol is set up so there will be < 5% free oligo or free antibody. We recommend that you analyze your conjugates, at least initially, by gel electrophoresis. We recommend a 5–20% gradient gel developed with Coomassie (for protein) or silver stain (for oligo.) That will tell you how well the conjugations worked.