I'm not sure about the reason of the problems which you described. Free jqGrid with Bootstrap GUI stile without jQuery UI CSS is not yet final, but GitHub contains already version, which it relatively close to release. I created the demo which uses guiStyle: "bootstrap". The current restriction of guiStyle: "bootstrap" is the usage of iconSet: "fontAwesome" additionally.
To customize the color of jqGrid CSS one need just specify border color or background color. For example I used the following CSS rules in the demo: