By the end of 2003, downtaking of most of the south elevation to the level of the vaulted chamber was complete. Rebuilding using the original stones then took place, and by mid April 2004, the elevation had been reconstructed to the top of the second storey. This allowed the roof beams of the great hall to be put in place and a temporary floor for the second storey to be laid on these, in order to facilitate internal restoration at this level. As rebuilding of the south elevation continued, placement of the roof beams for the second storey and and the laying of a temporary third floor was carried out.

By July, a temporary floor had also been laid in the vaulted cap-house ("John Knox's Room"), and thus access was possible to all of the tower's original rooms for the first time in over two centuries (Great Hall, Vaulted Cap House). With this, restoration of the south elevation, with the exception of the chimney, was complete, and placement of the roof timbers was being carried out. Between August and October, external work to make the structure watertight for the internal winter work was completed. The roof was slated, most of the exterior was harled, and the chimney on the south elevation was restored to its previous height. The harling was a pale sandstone pink (from the sandstone used in the mix) although the final colour would depend on the lime wash used at a later stage. Also, at this time a decision was made on the access to the area at the top of the stair tower; two of the features which had been lost were the parapet wall at the top of the tower and the original cap house which would have provided this access.