I was running into problems with the bowden setup and wanted to avoid putting the motor on the extruder (seemed too heavy). A flexible shaft seemed like a good solution...and lo and behold, as usual with my brilliant ideas, someone had beaten me to it and already generated a working version (kudos to the designer, I shamelessly stole the aspects I liked and incorporated them in this setup). Unfortunately the 'fix' was for the ultimaker2 and it required buying worm gears (similar to https://www.youmagine.com/designs/modular-printhead-ultimaker-flex3drive-merlin).

Here is a version that fits on an ultimaker original and ultimaker hot-end.

Print out all the parts, file down the teeth on the gears so they fit, and use a lubricant for final assembly of the worm gears (vaseline mixed with graphite seems to work well with PLA).

The flexible shaft (OBI house brand, dremel-compatible) needs to be taken apart and you end up with one flexible metal shaft (about 3-4 mm diameter, with a square end -> that goes in the worm gear; cut it to size and attach the other end to the motor coupling). Thread the flexible shaft through the bowden tube (which you no longer need for filament) to add stiffness and avoid supercoiling. The two scavenged bearings go on the top and bottom of the worm gear.

To get the whole thing to work you will also have to change the stepper setting (in hardware) from whatever the default jumper setting is to a ~4x increase; after that generate a new firmware for the ultimaker with the corresponding feeder settings and you are good to go. I'm sorry I forgot what my precise settings are, otherwise I would have stated them here.

The closeup of the worm gear shows the quality of the prints I can get with the current design; it's not really an improvement over the stock head+feeder, but now I have no more troubles with filament grinding or warping within the bowden tube with flexible filaments.