I'm now using bootstrap-loader package. With it you can configure which parts of Bootstrap to use with styles and scripts configuration options. Most likely it mimics what you can select on Customize Bootstrap page. Most of it is self-explanatory. But not all.
Considering styles. You most likely need mixins. They might be used by any other part of Bootstrap code. normalize also looks like thing not to disable. Then, scaffolding... What exactly is that? component-animations? Probably, it's best not to disable. close? I can disable just close buttons? Probably, better leave it enabled. utilities? responsive-utilities?
Considering scripts. transitions? collapse? Which parts of Bootstrap use them?
In other words, which parts you most likely don't want to disable? Especially the ones you might not notice right away. Are there any nonobvious relationships between them?