Auditing user behavior in a small organization to prepare IT restructuring

My company will be working on restructuring/rethinking the whole IT infrastructure for a small company (about 25 employees). A part of this is a migration to Google Apps for email, calendar, etc. That leaves many other things to think about (file sharing, business processes, etc.).

Is there any "best practice" way to gathering data from users about what are the actual pain points, what needs to be improved, of a more "scientific" way than simply asking/guessing?

I was thinking of running a software usage monitor such as RescueTime for each employee (with their approval), during, say, a week.

What are the other means of assessing user needs when given the opportunity to make as many changes as needed to IT infrastructure?