I applaud your jurisdiction for attempting this, however there are many pitfalls. Mainly, the largest one is that going to a outcome-based or zero-based or whatever you want to call it, is going to upset the current apple cart. Many departments and people are going to be upset if their department or program is seen as not being overly cost-effective. The elected officials need to be able to rely upon the data to determine if departments are doing more with less, and then they can put resources to the areas where they are most effective.
The State of Washington has attempted something similar, the Priorities of Government, and during the boom times it appeared to work, but now that revenues are down, the Legislature and the Governor have abandoned it because to truly be effective it will affect certain constituency groups.
I did my thesis on performance-based budgeting for my MBA, and it is a tremendous tool for government, but it adds a large amount of time on the front-end of the budgeting process, and without stakeholder buy-in it is doomed to failure. Don't get me wrong, I love it, and when I was an elected official myself, I attempted to utilize portions of these ideals, but I ended up offending too many constituency groups, so other elected official's in my county were afraid to utilize it.