Rough first layer and horrendous upper layers

I'm using a converted makerbot clone running marlin and slicing with slic3r.

Here is what my first layer looks like: [drive.google.com]

Here is what happens at the upper layers. The parts that look horrendous started as soon as the printer started printing solid infills instead of the 25% infill section. It almost seems like overextrusion but whythen is it only occuring at the end of prints where the printer is starting to close off the print with layers of solid infill?
[drive.google.com]

Here are my silc3r settings: [pastebin.com]

First layer: Maybe a tiny overextrusion, and/or bed distance maybe 1/10 or 1/20 mm off.
Upper layers: Too fast, too hot. Material? If PLA, your part cooling fan should blow at 100%. If ABS: print slower, give the layers time to cool down before printing the next layer. Print more than one of these objects at once.