We loved the grid, the form elements and buttons and its sized. The first thing we re-did was the nav bar though. Apart from that we think the framework really accelerated the design process.
I've been using it on new projects, but always found customizations a little awkward. Are you changing the actual bootstrap files (typography.less or whatever) or simply overriding them in your own style file?
I'm used to 960GS so I was at home when it came to bootstrap. I spent some time reading the examples provided, then started on a clean slate. Top nav, the mast then footer, then finally the main content. That way you are not technically tweaking their templates. You are branching out.