If your organization has 5,000 employees, it is apparent that they would have been recruited for some 'Job Positions' which had pre-defined 'Job Descriptions'. Your exercise, it seems, is the alignment of people to the business objectives, thus ensuring goal-based accountability at all levels. Balanced Scorecard (BSC) is the tool utilized by most organizations to achieve such alignment. Coupled with that, attitudinal transformation may be needed in some people where resistance to change is the vital problem to be addressed.
The approach discussed above by you and Mr. (Cite Contribution) is meaningful since to achieve any worthwhile alignment, Vision, Mission, and Values have to be the starting point. But job design and job analysis, leading to competency gap analysis of employees, need not be the next step. Maybe the identification of 'Core Competencies' as per the business of your organization is the next step. These are the competencies required for all 'white-collar jobs'. For the same competency, the definition, however, may vary as per the job levels. For example, if 'Drive for Results' is a core competency, it may have a 'strategic focus' when applied to higher-level job positions (like CFO, COO, Corporate Head HR, and other Functional Heads) as compared to junior-level executives (in different departments) where the focus may be purely operational. For middle-level positions, the definition of the competency 'Drive for Results' may cater for 20-30% as strategic and the balance as an operational role. Like this, one may pick up about 6-7 core competencies initially and create training programs to develop these competencies for junior, middle, and senior-level employees in the organization.
In addition to the core competencies, 2-3 special skills required for people in each department need to be identified. Training programs to develop these skills have to be designed.
While the design of BSC for your organization is being progressed by experts, training of people on core competencies and special skills has to begin simultaneously, so that a message travels across the organization about the launch of a 'strategic change process' by the management.
Well, you do need automated systems to manage these change initiatives. 'EmpXtrack' is one such system which has already helped many organizations to successfully achieve alignment of people to the organizational objectives.
Any queries that you may have on the approach suggested above may be shared to get responses based on the experience of experts.