The organ was tonally recast in the mid-1980s. An initial consultation survey at Easter 2001 was geared toward assessing musical conditions and developing recommendations for tonal restoration, reconstruction and possible augmentation. During the course of mechanical survey, significant termite damage was uncovered in the chamber containing the Great and Pedal. After the situation was stabilized, consultation work progressed to assisting with negotiations for damage settlement, drafting a workscope and request-for-proposal, and eventual awarding of the restoration work to the Spencer Organ Company of Boston.

At this juncture, the church requested a change of role from one of consultant to tonal finisher. Concurrently with the rebuilding of the Great and Pedal, samples were set to determine the extent to which the tone might be returned to a better resemblance of the 1935 aesthetic. Shop voicing took place in summer 2002 while the Great and Pedal were being rebuilt; pipes and mechanisms were returned to playability in November 2002, and site voicing completed in June 2003. As part of this phase of work, the two Great mixtures (which had been replaced in 1984) were exchanged for vintage Aeolian-Skinner mixtures to better suit the scheme. All tonal work was carried out by Jeff Weiler and Jonathan Ambrosino.

The church is now raising funds to complete the rebuilding and tonal reconstruction in the Swell and Choir, as well as a few additions to the Great. Richard S. Houghten refurbished the console from Aeolian-Skinner 1082 (Christ Church, Bronxville, New York) and installed it in Memphis in the fall of 2008.