The upright illumination has been corrected. The parts are available from a post about bug fixes on the Openflexure Microscope V7.0.0-beta1 released thread.
The current master build will have this and all of the other approved recent changes - although it also is not a tested release, so be aware of the notes on the Openflexure current build is here! post.
The cable does need to be long. 300mm is specified for the Upright, but that is for the version with the low-cost optics of the Pi camera. With a microscope objective and lens tube the camera is quite a bit further up. It probably needs 400-450mm. In my standard upright build the cable is reasonably out of the way and not too vulnerable in use. A cable slot would be useful, both for the camera cable and the motor cable. but there do not seem to be simple places to put one. Unfortunately your sketch would put the cable through the z-actuator mechanism.
The stepper motor just mounts on the upper z-axis instead of the z-axis in the main body. Autofocus then works as normal.
This might be trickier. Dark field is not well documented in general for Openflexure. The most complete instructions are for the LED grid illumination. That fits on the illumination dovetail in the standard inverted configuration. The upright configuration needs to fit the illumination on the optics dovetail, which is different. apart from the mounting difference, there is also less space to fit a large illumination array.