I need alittle help getting my parts to print to an accurate size so that they fit together properly.

For the most part, my prints come out looking good, small issues here and there, but visually, they are not that bad.
Its when I goto assemble parts that I run into an issue. Things are too large. If I print something from Thingiverse that has several parts, odds are they will not fit together.
I either have to shave/sand them down, or print the inner parts again slightly scaled down.

I saw this calibration post on Thingiverse, but I dont know how to make the proper adjustments to correct the issues.
http://www.thingiverse.com/thing:52946
I use CURA software for my prints, and really would like to stick with it.
Do I make these changes somehow in CURA? Or are these settings that are located in the firmware, similar to ESteps?

So far I have calibrated my ESteps, and made sure all bolts and belts are tight on the printer.
I also have Auto Bed Leveling setup and working well.
One thing I plan to try is to move the axises a set amount and try to measure how far they move, just like calibrating the ESteps

Printer is a Prusa i3v 10"
I generally print with PLA @ 190 and Bed @ 75 with a fan. Print speed of 75.
Here are some prints I have made so far, oldest at the beginning of the gallery, most resent ones are at the end of the gallery.
http://jtice.smugmug.com/3D-Printing/Misc-3D-Prints