Hi Mike, thanks for the quick response.
With the original app, we were using pure bootstrap names with customizations, plus a large number of new app only names as well. So yes it's a specificity issue that I'm running into as the unaltered rules in the default theme are conflicting with the same names on our theme. The variables aren't posing a problem. I'll keep reviewing to see if I can get more specific before going nuclear, thank you for clarifying that for me.
Regarding my other question about compiling our CSS externally. I'm currently loading the .css file using the @import "./styles/main.css" within the /imports/plugins/custom/app-theme/client/index.js file. I've noticed the system loads the CSS as an internal stylesheet. Any way to keep it as just a linked external? Would this avoid the 20-30 second app refresh?
Almost forgot, we're using SASS bootstrap 3.