Bootstrap is great for getting your projects up and running quickly and having them really shine. Upgrading... that's a beach!
However... if you started with a cloned a version of Bootstrap, made some variables.less updates here and there to get your colors just right, added in your own Javascript goodies or maybe you just got crazy and recreated your whole company blog using Bootstrap... way to go!
Let's suppose there's a new version of Bootstrap that fixes those pesky issues you've been waiting for, now it's time to integrate those changes into your totally custom site. If you've got this solved, let me know! ...but for now, here's my solution.