Problem: Serial connector hits cape
Problem Solved!
I design electronics, so the nice folks at Samtec sent me a few stacking connectors as samples, but they are available for low-volume purchase as well. Official connectors from the BeagleBone SRM are also available via the Major League BeagleBone store:
Samtec SSQ-123-03-T-D
Major League SSHQ-123-D-08-GT-LF
The next issue is BeBoPr specific. Since the BeBoPr was designed for the initial BeagleBone white, it happens to overlap with the HDMI and eMMC pins. Even worse, the two board enable signals are mapped to eMMC pins that are active during boot, meaning if you have a machine hooked up it could exhibit strange behavior while the BeagleBone Black is booting. One solution is to *REALLY* make your BeagleBone Black behave like a White, but this requires changing boot resistors soldered onto the board and using a custom-built device tree. The easier solution is to apply the ECO developed by the board designer that moves the enable pins away from the eMMC pins that wiggle during boot. Note that my mod does not look exactly like Bas' because I tied pins P8.5 and P8.7 together on the stacking connectors instead of on the BeBoPr, but it's the same mod. My LinuxCNC configuration is setup to drive both the old and the new enable pins, so it should work regardless of which 'Bone you're using and whether or not you've applied the ECO.
Finally, the BeBoPr does not have any provisions for connecting additional circuitry, such as a character LCD or an encoder as typically used in an Arduino based 3D printer as a stand-alone interface. You could solder wires directly to the 'Bone, BeBoPr, or the stacking connectors. However I recommend a breadboard cape, the very cool breakout cape (which also solves the problem of the serial port header interference), or since the 'Bone headers are on a 0.1" grid, just do what I plan on doing and use old-school perf-board from the 'Shack (get whatever size you want, there are several choices). NOTE: For everything but the breakout cape, you will probably have to cut/trim/drill to provide clearance for the serial header and possibly the parts on the BeBoPr board. Break out the Dremel! :)
Stay tuned, I may be adding a section on getting HDMI working with the BeBoPr, but that will require moving a lot of pins.