It has been a few years since I build the Mendel printer and the lack of a user friendly software made it very hard to even figure out if it was calibrated okay. I put the project under my desk until now!

I found a new software; Repetier from Repetier Software (Duh!). It support many versions and hybrids of 3D printers and even if my Mendel Gen6 is a bit old now, it works fine.

Repetier also converts the STL to G-Code with a very intuitive user interface. I had to reduce the default speed for everything by a factor 2 to not stall the stepper motors, but I'm still tweaking the temperature and flow speed to get the X and Y dimensions more precise.

From the beginning I calibrated the extruder's Z axis to the board surface and I discovered that the first layer star at Z=0. By offsetting the Z-axis with approx 0.4mm I got the first layer more correct.

I was mistaken... The nozzle had become lose and was scraping the board. After I tighten the bolts I could remove the Z-Offset again.

Now I have another problem with stalling motors, but I suspect it to be of the mechanic nature. It is only the Y-Motor that stalls, what seems to be randomly.

Update:
The belts where to tight and made the motors stall. After I loosened them up a bit I could increase the motor speed  without stalling.