inner diameters vs. perimeters

About the only thing you can do is reduce the number of perimeters to something less then the wall thickness of the tube your trying to print then set infill to 1.  It will zigzag in-between the inner and outer perimeters and the part is still solid.  Either way there is a good chance the inner won't be perfect but it will be from the expansion of the ABS not because the nozzle didn't follow the correct dimensions.  If that is a problem you may have to fudge the inner diameter of your design.  The good news is you should be able to test by printing just enough to measure and then adjust until you get the desired results.

It does to a point.  Let's say you want to print a line with 1 perimeter that  is 1mm.  The Slicer is going to draw 2 lines but your extrusion width is set at .48 so you'd get a line that is really .96mm so the .04 has to be made up with infill to get to 1mm.  That's fine until you try to go the other way.  For example you want a .90 line and the two lines equal .96  Slicer isn't going to tell the lines to overlap to reduce the width to .90  instead it is going to draw .96.
The problem is when you get into circles this is compounded by the fact that that .06 now becomes .12 less diameter.  If your going for precision and the part is small this can become a problem.  Most times for stuff like the OP is doing a good drill bit is the easiest way around the problem.  Of course if you want a part that is just perimeters and no fill then they need to calculate out to an even multiple of your extrusion width.  This isn't always an option so your left with what I stated above. 
Then there is the obvious most of our printers just aren't calibrated with a level of precision to make any of the above that important so we figure ways to work around it.

Wouldn't the inner holes be determined partly by amount of perimeters (if let's say it's a smaller object and the holes aren't far away from the perimeters) .. so if so what is the perimeter setting I should be using to insure the best sized inner holes.

also when calibrating steps per MM for X and Y what should I be measuring for accuracy, the outer dimensions?

Ok. Is there any benefit to using more perimeters than the default slic3r of 3? Or less?

Attached is what I'm gonna try out for x/y steps-per-mm calibration. The edges between the cutouts should be 50mm, and the cutouts are there to make sure the backlash has been picked up prior to starting the edge. Should be easy enough to measure with verniers. There are probably a million other options too, up to you.

If you want to do a 100mm one for extra fun, just scale the thing up 2x in repetier object placement window. Personally I'd be worrying more about curling than relative errors in my setup, it's all a bit hit-and-miss at the moment.