I have retraction, coasting and wipe on already, and 'only retract over open spaces' is off. That being said, the extruder shouldn't be retracting all over the print like this - the exterior is a few lines that print continuously, with almost all of the moves inside the part. Could S3D be generating spurious retract commands?
I'm pretty sure that it's not over-extrusion - the large majority of the surface area is fine, so it's not generally over-extruding (i.e. the filament diameter and steps per mm are fine). The problem is the blobs that appear in very specific locations for some reason. The blobs are actually only a few percent of the surface area, and fairly large areas are completely smooth, so it's triggered by something specific.
It also happens on two different printers (a Replicator and a FlashForge) so it's not an individual machine's hardware. They're both running Sailfish, which might be relevant. And the "pimples" occur with S3D but not MakerWare, on both printers, so I'm thinking the difference has to be the software, not the printers.
In my experience, these "pimples" are caused by the printer briefly stopping instead of moving continuously, such as by the controller being able to keep up with the command stream causing pauses while it catches up, so too much plastic is extruded. But I can't figure out why the extruder would be stopping all over this print from S3D.
I'll try making extraction more than 1mm and see if it changes anything. Perhaps I'll get lucky.
And yes, as I mentioned, active cooling will help with the drooping at the top. But it's not related to the blobs.