to stop the dragging across your print, there is a setting for printer under filament>retraction>z lift make sure this is at least .2 taller than your layer height. I dont know if it affects the height when its finished printing, but i also have my Minimum Travel Requiring Extrusion amount set to 20 mm. Also be sure Wipe before retract is not checked, and retract when changing islands. If non of that works then you can add this to your Printer>custom g-code>end g-code.
G1 Z5 F5000 ; lift nozzle
Also to adjust your extrusion, are you using the tuning adjustment under controls. Or do you go to the filament>extrusion>flow>extrusion multiplier.
You may also want to check your printer>extruder>nozzle diameter is set to the correct size.