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for Z axis there is mechanical calibration described in chapter: http://reprap.org/wiki/ToyREP_Build_Manual#Print_Surface
It is the very basic way and you can do it differently, like start with measuring the height of X axis rod from table on both ends and than level the heatbed surface by driving the hotend into corners and using the piece of paper method.
In firmware, the calculation of microsteps per mm is in: http://reprap.org/wiki/ToyREP_User_Manual#Speeds_and_units
It is motor_steps_per_turn x gear_box_reduction * microstepping / pitch of the threaded rod. in case of 28BYJ-48 with bipolar hack, with 1/4 microspepping and M5 threaded rod = 32 x 64 x 4 / 0.8 = 10240 microsteps per mm (or as in the example with 1/16 microstepping 32 x 64 x 16 / 0,8 = 40960). You will have to print few layers of known height and measure the overall height of printed model, than use the same formula from Wiki
Your recalculation of X and Y seems correct. Keep in mind, that this is influenced by size of printed pulley and tension of belt, so it is perfectly OK that these two numbers are not the same.
In Z axis where is no tension or printed part involved, the basic calculation is usually correct unless you have for eg. motor that do not have gear box with 1:64 but some odd number like 1:63.68395. Keep in mind that if you print for eg. the 10mm heigh calibration box, and slice it with 0.3mm layer thickness, the height won't be exactly 10mm but rather multiplication of either 33 or 34 layers, means 9.9 or 10.2mm. Pronterface will write the actual hight in the status bar on the bottom of the window. For better results, You will have to print something taller than the calibration box in all four corners of heatbed (it do not have to have infill and top layers to save filament and time). Chose one corner as the reference, calculate the difference between corners and make this correction by the M3 screews in corners. One full turn of M3 screw should do 0.5mm height difference. Than use the reference corner height to change the microsteps per mm in firmware and you will be good to go.
For extruder, you have to measure the length of filament, that is coming INTO the extruder, so mark like 50mm and 100mm on filament above the extruder (for eg. measure from top of the extruder) then extrude 50mm in Pronterface (or other software) and measure the length to the second mark. If you will measure for eg. that 53.5mm is left to second mark, than you extruded only 46.5mm. Put this number into the equation and you will get the right number of microsteps per mm. Make new marks and recheck, It should be better but probably not perfect. Some deviance will be always there due to the precision of printed extruder gears.
Later on you will set extrusion multiplier in Slic3r (or Cura) settings. This is to correct the heat expansion and flow of the plastic when printed. For PLA I use something between 0.9-0.95 (90-95%) and for ABS 0.975-1.0 (97.5-100%). These numbers are very dependent on plastic properties, that are very different for every manufacturer and even colour of the filament. You will have to tweak it depending on the print results you will get with the particular filament. For eg. if holes will be printed smaller then required it is probably due to overflow so the multiplier needs to be a bit lower. On contrary if layers on surface seems to have occasional space in between go a bit higher.