What setting do I need to change to get rid of this gap between the shells and the inside?
It's generally called infill overlap. 
In terms of first layer it's good to set extrude rate to 120% or even more so infill will overlap perimeters and itself. There is also the issue of "overlapping" layers which is not managed by any specific parameter. it's the issue of layer thickness and HE temperature.

Unfortunately Matter Control has kinda bug or at least an issue with extrude rate. If you set higher  extrude rate then overlap will be automatically reduced in some way. So it's good to increase extrude rate manually during printing and then set it back to normal. this will cheat slicer.