Dear Theresa,
I was interested in your question, we are a specialized Windchill customization/extension company and we have spent two years developing our custom build and install process for Windchill. We have decided a long time ago to move away from the monolithic approach (like BiF) and using VMs and move to an apps idea, where we work in a much more distributed way which has been very sucessful. One thing we noticed early on is that a dev environment for customization is not the same as the classic software development model and we adapted our processes to adjust to that. The concept of one build for a lot of often disconnected pieces of code never made sense to us.
FYI - We use Jira, Ant, SVN and OpenOffice server and as tools within our build process
BR
Simon