For the gaps in the top layers, you should read this link:
https://www.simplify3d.com/support/prin ... top-layers
As I mentioned above, you should also increase your "outline overlap" percentage on the infill tab. Whatever value you have it at now, I would add about 15% to that. S3D's great print quality guide also explains this one:
https://www.simplify3d.com/support/prin ... nd-outline
Correct those issues first, and then check to see if the holes are still too small. If they still are after everything else has been fixed, then go to the Advanced tab and you can use the "horizontal size compensation" setting. For example, if you make that setting -0.05mm, the walls will all shrink by 0.05mm, which means your holes will actually EXPAND by 0.1mm (2*0.05 since there are 2 sides to the hole).