I think I solved my problem. I couldn't get the Retained earnings to go away on the Balance Sheet. I was using the Automated Schedule M-2/Retained earnings Worksheet. When I checked "No" to that option on the 1120S page 5, I could then just delete the Retained Earnings balance and enter the Additional Paid In Capital on the M-2 - Other Additions.

Everything looks good now, even the Basis statements.

Thanks for all the help!