I have a customer that is a signer on a corporation account. This individual is also owner of the corporation. He withdrew $25,000 in cash from the corporate account for personal use. On the CTR would he be the only individual named on the CTR using Part 1, 2a person conducting transaction on own behalf? Or would the corporation also be named in the report? If so where?

He simply cashed a check and only he goes on the CTR - no different than him personally cashing a check drawn on a non-related entity.

Would you still check Negotiable Instrument cashed(27d)?

Yes.

And, because the check is drawn on your bank, list the account number in the appropriate spot.