It's also possible that your printer's buffer gets overridden when you get to the end of a print - I've seen some printers that do this. Try adding M400 as the first line of your ending script.
Uncheck the option "Only retract when crossing open spaces" and it will retract there. It will also retract every time the head makes a non-printing move, but that's the only way to make that work at the moment. Add your voice here perhaps? https://forum.simplify3d.com/viewtopic.php?f=9&am...
I think coasting would help a lot to get rid of your blobs at the seams. Try enabling that with ~1mm instead of negative restart distance. You can manually enter a smaller value for extra restart, bit I personally try to avoid it whenever possible because it can be very bad when you do small detaile...
Most likely a limitation in the printer firmware. Take a look here for info on configuring sailfish (the firmware that your printer uses): http://www.sailfishfirmware.com/doc/
Just guessing on the preview (factory files are the most useful thing!) that you have the support pillar resolution too high. Reduce that or manually add in supports and you should be good.
I've seen this before, I think on the forum here but I can't find the thread quickly. The raft settings get shared between parts if they're close together enough. Spacing them further apart fixes it.