Glad you're enjoying the software so far! Let me see if I can help answer a few of these questions.
1) The output path for gcode and x3g files is actually saved each time you browse to a new path. So if you always put all your gcode files in the same location, the software will automatically remember that location for the next time you export a file. It's basically a dynamic method for saving your output location without having to hard code or bother with another setting.
2) The toolpaths coming out of Creator are heavily optimized, so it's not uncommon to see a 30% improvement in printing time compared to other slicers. That can add up to BIG savings if you're doing an 8 hour print like you said. And it's even better than it was able to generat these highly optimized paths with the 10x faster slicing that you noted
3) I think I sent you an email about this topic as well, but I suspect the vibrations are either coming from reduced printing speeds (usually to maintain adequate cooling) or maybe even some very thin infill segments. If you want to post your .factory file (File > Save Factory File As...), I would happily take a look at your current settings. The factory file will contain the STL, placement information, slicing settings, support material, etc. It let's us recreate exactly what you were doing which is extremely helpful for troubleshooting. The files are also highly compressed so it saves A LOT of disk space using a factory file versus sending the complete gcode file.
4) And if you are running into over-extrusion issues, the easiest thing to do is decrease your extrusion multipler to reduce how much plastic is used for a given line length. I would try that before modifying the filament diameter. The default Rep2 profile is pretty good though, so you shouldn't be too far off unless you are using a very different material or filament manufacturer...
Hope that helps!