Hi There
It looks as if it printed the large area reasonably well, but went wrong when it had the smaller areas to work on. This looks as if the extruder was slightly clogged, and/or the hobbed bolt started slipping.
To start with, always set up the backlash of the extruder gears with some filament in. This will push the hobbed bolt sideways and will tighten the mesh of the gears. Check that the pinch bearing holder is free to move properly. If you didn’t file down the ends of the bolt that holds it together, they can rub on the aluminium sides of the extruder head. The holder can move sideways a bit, so if the bold protrudes, can stick part way through a print. This allows the hobbed bolt to slip.
I would recommend making a spool holder with bearings for the filament. Any extra force needed to pull the filament can help to make the hobbed bolt slip. You always start a print with the filament fairly loose on the spool, and it will tighten up as the print progresses.
Alter the retraction distance in the slic3r settings. Take the distance down to at least 1mm. I think the default was 4mm. If the hot end of the filament is retracted too much into a cooler part of the extruder, then that may cause it to stick. the hobbed bolt will still try to feed, but instead it will grind into the filament. It might restart again, but the bits of the grinding will cause it to stick further on - and so on! Also the extra retraction amount will cause extra wear in the filament if there are a lot of retractions close together in time. This will also cause the hobbed bolt to loose traction.
The hobbed bolt itself is not perfect. Other people have used a Dremel to sharpen the teeth. I personally put in a Hobb Goblin bolt from E3d. No problems with slipping now.
The other problems can be caused by the action of slic3r. When the print requires a lot of small zig-zag movements to fill up a small area, then the amount of filament around the nozzle can cause a bit of back pressure up the nozzle and cause a partial blockage.
Try slowing the print speed down to allow the filament to lay down properly in these small movements.
I find that Cura is better in many ways to Slic3r. The movements required by the printer seem much more gentle, and the honeycomb effect that shakes the printer (and makes your teeth rattle) is replaced by the quieter criss cross pattern. The small zig-zag movements are different too, thus helping to keep the nozzle clear.
One last thing - filaments vary quite a bit in quality. I am hooked on Rigidink, which seems to be very stable between reels. But some filaments can be nothing but trouble.
You will now have information overload! Don’t give up though.
Happy printing
Peter