I think you have your words mixed up. It is not possible to set different shell thicknesses for different parts of the model. Also shell thickness has nothing to do with infill. You need to set your nozzle size to 1.0 and make your shell thickness the same or a multiple of the nozzle measurement. If you are looking for solid infill at the bottom then you need to check your initial layer thickness and layer heights and check they can add up to the thickness you have set for bottom thickness. After that if you have not set 100% infill you will get lines.
Not sure I understand your question, but first, what version on Cura do you use ?
In the latest stable version (15.04) you set nozzle size on the advance tab, set this to 1.
Obviously the the print lines will be further apart from each other when you set 1mm iso 0.4 mm. This is normal as the lines you print are wider.
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