You should have received our custom firmware to install on the printer (it would have been on a USB drive). This custom firmware should adjust those endstops.
Next, you will need to make sure your Cura system configuration (Machine->Machine settings) is correct for the dimensions specified in our Quick Start guide. We recommend Cura version 15.04.6 with the exert settings enabled.
For the issue with the printing tip, you will need to level the build plate before you get ready to print. Mount the Discov3ry nozzle, then select Maintenance->Build Plate from the printer menu and follow the prompts. We recommend using a standard business card as a gauge. Rotate the button on the front of the printer until there is just a small bit of resistance between the nozzle and the business card. If the friction between the business card and the nozzle causes the nozzle to wiggle, then it is too close. Do this for all three stops on the build plate, and then it should be good for printing.
The other detail to make sure your first layer prints nicely, is that you must get the nozzle primed. You run the Purge Fast or Purge Slow print files for this. Once the material exits the nozzle, let it keep running another 2-3 minutes to build up a little excess pressure. Then power off/on the printer, and select your print file, and it should be good from there.