I just finished building my Rostock Max V2 -Night Fury- (I need to update my building log: http://forum.seemecnc.com/viewtopic.php?f=42&t=5814), and started the daunting calibration process. But, instead of going down with the typical back and forward adjustment of the endstop screws, I used EXCLUSIVELY EEPROM values to get the bed flat.
Maybe I was just pure lucky, but after about 15 - 20 mins calibrating, I got it right. You can see, this is the first print EVER for my new Rostock. Take a look, the bed is FLAT. Never get this flat as easy with my old V1, using the original procedure. Of course, it has to be that the new V2 is more accurate in is build than V1 as well.
Here is what I did. It is very similar to Geneb's procedure, just using the EEPROM instead of screws and doing some simple calculations for Horizontal Radius.
Before anything, started by getting the Z-Height right (using geneb's procedure described in manual). Then, start the calibration with Z tower:
1. Ran the "Script 1" (or whatever script you are using for Tower Z) to get Z tower height. Yes, you should set Z5 or so the first time, just as a precaution to avoid hitting the borosilicate glass

2. Using the "Z position" option from Advanced Settings menu, move the nozzle until you get it down to the bed (yes, use the paper method). Then write down the offset value for this tower. In my case, it was -1.15 mm.
3. Convert this offset value, from mm to steps. For this, get the "steps per mm" from the EEPROM (it is 80 for my V2), then, simple multiply this value by the offset in mm, then, invert the sign of the result (or, simple, multiply it by -1) this is
-1.15mm x 80steps/mm x -1 (just to invert the sign) = +92 steps
4. Get current value placed in EEPROM "Tower Z endstop offset [steps]", then, and add this to the value from step 3. For the first iteration, the original offset value would be ZERO. However, in the following calibrations, this value would be the previous offset entered. I was in my second calibration, then the original offset was 200 steps
The new offset value would be:
200 steps (original offset value) + 17.6 steps (current offset) = 217.6 steps (new offset)
Store this new offset in the EEPROM variable, overwriting the original value.
5. Re-run Script for Tower Z, and re-asses the offset. It should be zero, or very close to zero. If it is not zero, then get the offset value in mm (as in point 2) and then convert it to steps (as in point 3) and re-calculate the new offset value, as in step
After Tower Z is OK, repeat the same points from 1 to 5 for Towers Y and Z.
6. Now, run the Script 4 (or simple G28 followed by G0 Z0) to get the Z-height. As you know, it could be above or below 0 (NEVER zero

Now, as explained in Geneb's manual, you have to modify the value in the EEPROM for "Horizontal Radius [mm]" by 0.5 (adding or subtracting it to the original Horizontal Radius).
7. Get back to re-calibrate the towers, but this time, you do not need to adjust one by one. You can get the three offset values first, and then enter all of them at once in the EEPROM (remember to invert the sign and to add this value to the original offset value in the EEPROM). You can do it one by one, but if you do it at once you can time.
8. Get the new Z-height (G28 + G0 Z0 or script 4). If not zero, then get the current offset (again, using "Z position" option). Then, get the variation in offset from the original one (from step 6), and the new one.
Delta = Z offset Step 6 - current Z offset (Important, get the absolute value => NO SIGN!)
Use this delta to calculate the new new Horizontal Radius:
New Horizontal Radius = (0.5 * current Z offset) x Delta
NOTE: this DELTA value is the mm that your nozzle will move with 0.5 variation in "Horizontal Delta Radius", it is important to write it down, as will help you to speed this process in the future.
9. For me, it was all, at this step my bed was flat.
I just finishing a second print (actually, the third, as the second ended when I tried to read the EEPROM to while printing

and, here is the calibration cube -third print!- (25mmx24.95mm x 25.06mm):
Not bad For sub 30 mins calibration. I am loving my Night Fury!!

I will try this for my "old" printer and report back if works the same ... but has to be other day

Cheers!
Art