@smcelm , I guess I'm not understanding the ownership structure of these companies. When you said that "you" made the employer contributions, it seemed to suggest that you were 100% owner of these companies. If you are only 3% owner of company #1, unless this company is a qualified joint venture with your spouse and your spouse owns the other 97%, it would seem that the company is a partnership that should have made the employer contribution and reported it in box 13 of Schedule K-1 (Form 1065) which would transfer to the Keogh, SEP and SIMPLE Contribution Worksheet from your entry of the Schedule K-1, rather than you making a separate entry on that worksheet.
If both companies are actually disregarded entities, it still seems like your contributions would be subject to a single contribution limit as one self-employed individual, a single entity, not unrelated employers.
