On the cylindrical part of my model it's adding infill where it should be just circular lines, it makes for a very shaky print during this area. How can I make S3D just go round and round until finished? Hope I'm making sense.
1) You don't have concentric infill selected (may help)
2) If the gaps between the perimeters is not a multiple of the extrusion width then it cannot infill with a single extrusion and will create a wavy infill. Eg. if the extrusion width is 0.4 and the gap is 0.7 then it can't lay two full extrusions, so it will have to fill the gap with a wavy fill or there will be a remaining gap.
I hope that makes sense.
NB. I know it's always said, but attaching a factory file would make the problem easier to diagnose specifically.