I'd suggest that if you're going to sql server, that you might want to consider changing that a bit:
- Meet with stakeholders over time to resolve information issues.
- Create a new schema for a new'n'improved system that includes all data.
- Harmonise data in the various databases. Create triggers that keep information harmonised following above schema. Run this way for a while to ensure that schema meets organisation's needs. Use this phase to refine schema according to users' needs.
- Implement new and improved schema on central high powered db. I'd strongly consider postgres (free licensing, support available from developers for money, it runs on Windows too, has ports to many versions of unix so when growth is such that windows keels over you can scale to a better platform with little pain).
- Move data into central db using above schema for organisation. Migrate clients to software to access this db instead of the group of old databases.
- Keep both old and new systems synched for a while to ensure that no problems pop up that require reverting to old system
- Decomission the old system.
Lots of folks here have more experience with this stuff than I do, I'm sure that they'll chime in if I've egregiously misrepresented/fucked up anywhere.