I've been tuning Marlin configuration, latest changes are in github.
I enabled Babysteps which is an option during printing where it's possible to do minor adjustments to Z, Y and Z axes.
I also enabled manual mesh bed leveling, but haven't used it yet because it doesn't understand that in Cube the bed should be rised near the nozzle, the bed is left at bottom and it's hard to measure the distance. Anyway the option seems to be similar to Cube's leveling option, but apparently Marlin uses the leveling values during print for leveling, like with autolevel feature.
I also ran PID autotune, which gave me new PID values and now hotend temps seem to be bit more stable.
One of the things i tried was increasing the acceleration values, but it seems that Cube is real bad at that. In one of the guides, a starting value of 3000 was suggested, but at least my Cube cannot do more than 500, Y axis skips steps (a lot) at some point, which ruins the print as Y coords move several cm...