The debug UART has both the uboot software behind it on boot, and later a 
linux serial console.

During boot, if your device emits any characters, this will trick uboot 
into putting up its menu and hanging the boot process.  It will be waiting 
for you to make a menu choice and your device will know nothing of it.

Assuming you miss that one second window, plus all the time preceding uboot 
coming up under power where the uart's fifo will be filled, then you will 
clear uboot.   But this is too much risk.

The next phase of the boot has linux hosing its console output to the same 
debug port, and depending on the linux setup, you may have a serial console 
come up on that UART also.  I do here.

So the debug uart port is difficult to use for anything but debug.  

Use another UART.  The device you describe may be using TTL serial, you did 
not mention RS-232 levels.  This should be confirmed.  If TTL, your device 
may still be at a voltage which is too high for the beaglebone to handle.  
Check the datasheet for 5V compatibility.  I doubt its acceptable.  If your 
device is assuredly TTL at 3.3V then it will probably work hardware wise by 
just hooking up the device, crossing TX with RX and tying GND to GND.  The 
3 wires you say.  Then you have to PINMUX in the UART's TX and RX pins, or 
pick a UART you know is already pinmuxed out.


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