I have a Prusa i3 with 3mm extruder and E3D v6 hottend with RAMPS 1.4 with Marlin 1.1.7 and I'm using Slic3r Prusa Edition with 0,2mm layer height and 2mm of retraction with ABS with heated bed at 110ºC and hotend at 250ºC.
I don't know why in some prints that are more complex than a simple calibration cube I get bad quality in some parts, usually small plastic particles around the piece (specially if it's an small piece). And this happens a lot in the last layers of printing.
The base has the name of the autor: Jacob Stanton. When I try to print are totally unreadable. But the rest of the print is relativelly well. I've tried to print the calibration cube and the size is 20,01x20,05x19,96. I've tried to extruder 100mm and exactly 100mm of filament is extruded. I think that the calibration is not the problem.
Is it realy a 0.35mm nozle ?
Could be stringing - 250C is the hot side for ABS.
Is this direct extruder or bowden? 2mm would seem reasonable for a direct extruder but you could try adjusting this higher - especialy as you have 3mm filament - not sure what difference that makes but its harder to get the flow rates matched with large filaments and small layer height/nozzle size. Thats one reason people use a geared extruder.
Problem seems to be on the small features so layer time may be part of the issue but i can't recomend anything to try for that.
You have seams aligned yet the blobs seem scatered so it may not be the retract thats the problem.