A "rifle screen" of 1⁄2-inch (13 mm) armor 3 feet (0.9 m) high was installed on the top of the turret to protected the crew against Confederate snipers based on a suggestion by Commander Tunis A. M. Craven, captain of her sister ship Tecumseh.

[10] Completion of the ship was further delayed by the low depth of the Ohio River, which prevented its movement from Cincinnati, in December 1864, to finish its fitting out.

[7] The ships needed a deep-water berth and were moved opposite Cairo, Illinois, in mid-1865, even though they still had to be anchored in the main channel, where they were often struck by debris, drifting ice, and vulnerable to accidents.

Tippecanoe's anchor chain was broken on 27 March 1866, when she was struck by a steamboat towing barges; the monitor collided with Oneota and the two ships were dragged 2 miles (3.2 km) downstream before they could be brought under control.

In August 1867, the Navy turned over Catawba and Oneota to Swift & Co., contingent on a guarantee that they would be returned in good shape if they could not be sold, and the company began refitting them for Peruvian service.

Gideon Welles, Secretary of the Navy, initially indicated that the company could repurchase the pair if it refunded the government's costs to build them, but changed his mind and said that he had no authority to do that.

[7] To prepare the ship for her lengthy voyage to Peru, around Cape Horn, Swift & Co. added a breakwater on the bow, stepped two masts with a fore-and-aft rig, to supplement her engine, and provided closures to make vents and deck openings water tight.

[14] While this was going on, the United States was negotiating with Great Britain over compensation for losses inflicted by British ships knowingly sold to the Confederacy during the Civil War (the Alabama Claims).

The ships finally reunited at St. Thomas, in the Virgin Islands, and had to wait for Pachitea to arrive from Peru, to tow Oneota, which had been renamed Manco Cápac, as the monitor had accidentally rammed and sunk Reyes during the storm.

While entering Rio de Janeiro, on the night of 15 September, Manco Cápac ran aground; she was refloated the following day, but the damage required three months to repair.

[16] Atahualpa was towed from Callao to Iquique, then part of Peru, from 11–22 May 1877, to defend that port from the rebel ironclad Huáscar during the Peruvian Civil War.