There's a sticky in this subforum that provides some help with calibration. Or, google 'marlin extruder calibration' for any of a number of calibration resources. The calibration guide by Triffid Hunter gets a lot of recommendations throughout the reprap community. The key thing to focus on here is ensuring that your extruder is providing the volume of melted filament volume that the slicer is assuming. You also have to measure your filament diameter and set that in your slicer since raw filament is rarely the exact correct diameter. You really should do this before trying to work through any print quality issues. If nothing else, the calibration process removes a few of the many variables involved in getting a good print.

I just realized the Pegasus doesn't have a Greg's Wade extruder, so my earlier question on whether the large gear is ever reversing won't make sense to you. I guess what you could do is lightly pinch the filament above the extruder and feel whether the filament is ever being pushed upwards. Your settings should cause the filament to move backwards 2.5mm for each retraction.

One thing you could look at is the distance between the columns in the print. Note you're telling the slicer (you might clarify what you are using for a slicer, including the version) to NOT do a retraction for move distances less than 3mm. Any chance the distance between columns is less than that? You can also look at the gcode file in a viewer like gcode.ws to see what the slicer is telling the printer to do, including where it is supposed to be doing retractions.

I'm leaving further support to the thread to others with Pegasus experience - I don't know how sensitive the Pegasus is to retraction extruder motor speed, etc. Good luck.