When you drew the holes did you take into account the nozzle size?
If you are using a .4 nozzle then you have to open the "hole" .4diameter, .2 radius. The slicer programs do not use any type of "tool size" compensation. Even then the bottom layer will be off as it is purposely mashed into the bed for better adhesion.
This should help you get more accurate hole sizes.
I am about 95% sure this is incorrect, slic3r has settings for extrusion width for first layer and then other layers. Cura has settings for different sections, infill, skin, support etc.
This affects how soread apart the lines are and obviously, their position.
Also, looking in the wrong place to calibrate, you need to look at the machine settings first, for instance my latest machine had steps/mm on the X and Y set to 81 when it should be 80.
My guess is they did that to compensate for PLA thrinking 0.5% but it is the wrong way to go about it, scale the print in the slicer by 0.5% if you have to, the X shoukd move 80mm if you tell it to, not 81mm.
You adjust the machine so it does what the slicervis telling it first, then toy with settings in the slicer to get the results you want, that is the point of calibration.
edit: the new central spar for my robot chassis just completed actually (2:45 print), the 2 bearings are 11mm outside diameter and are a push fit with a vice but can then be removed by hand, the central bush for the bearing to 6mm bolt needed rework, the outside is 8mm and I shoukd have designed it 8.2 to cope with shrink, it is a tiny bit loose in the bearing, the 6mm centre hole I had to drill out to fit over the bolt, the bit next to it is what was removed. A trick for drilling pla to not tear it up is to operate the drill backwards, then it will remove much thinner amounts of material.