When a signaling system reaches its end of life, an overall replacement is necessary. The replacement may be in-kind but for many mass transit agencies, it is common that capacity needs will have grown significantly, and the transit agency is required to increase capacity while tackling obsolescence. Capacity and obsolescence are the primary reasons for deploying Communications Based Train Control (CBTC) technology to replace conventional trip stop and track circuit-based systems operated by New York City Transit (NYCT) or cab signaling systems operated by Baltimore Maryland Transit Administration (MTA) and the San Francisco Bay Area Rapid Transit District (BART). Resignaling projects are often refereed as brownfield train control projects. Due to the technical and commercial complexity, the quantity of stakeholders, the number of interfaces, the regulatory involvement via safety certification, the temporal and geographic scale of the project and the continual evolution of the existing system, a robust Systems Engineering (SE) process is necessary to achieve success in large signaling replacement projects. This paper describes the software tools and processes that were deployed to meet the technical, legal and commercial needs of a large signaling replacement project during the specification development phase. The processes put in place were tailored to the size and location of the team members. The paper describes the software tools, such as IBM Rational DOORS, Microsoft SharePoint Online and Office 365 which were integrated and configured to allow for collaboration while accounting for the security, commercial and legal requirements of the agency. The selection, deployment and management of these processes and tools enabled the large, complex project to succeed.