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pi-top Proto troubleshooting

I've constructed an interactive box for an enrichment project with chimpanzees, and have several LED buttons interfaced into a pi-top PROTO.  A stepper motor HAT sits on top of the PROTO and relays to a stepper to dispense food reward pellets.  I have a pi-topCEED display and board also connected to my pi.  My programmer designed a button test to detect the buttons through their GPIO's in the terminal and only three of the 11 outputs are being detected.  When the stepper motor HAT is removed two of the buttons are no longer detected by the test.  Any ideas as to what's going on?  Is the PROTO not a good fit for the requirements of the task?  There are no obvious shorts on the PROTO.  I bridged the 5V power to the A-E/1-12 contact points for the positive leads of the buttons and speaker.  It's worth mentioning that the pi does not boot up properly unless one particular button in GPIO26 is held closed.  When this button is not held closed several buttons are lit but these buttons do not coincide with the GPIOs that are detected by the test.  Also, the button plugged into GPIO4 is continuously lit and will restart the pi when pushed.  I'm a novice and amateur in this area and have been receiving help in the construction of the box.   Attached are pictures of the setup.  Any advice will be appreciated.

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