Quote - this is bad news since my figure is largely dependent on JCMs.

The workaround it to pose your figure using IK, then turn IK off when you have the figure in the desired pose. When you turn IK off, the JCM should kick in, and the pose should remain almost the same, though there can be slight changes in the pose when you switch IK off. This usually works OK for static poses, I'm not sure if it works as well for animations, you might need to add keyfremes to keep things good.