My only other thought is to bypass the YunSerialTerminal sketch. Run a blank sketch (what you get when select "File | New" in the IDE) or something trivial like the Blink sketch - something that doesn't use the Bridge or Serial1 or pins 0 and 1. Load that sketch onto the Yun, and that will essentially disconnect the AVR processor from the Linux side.
Then, use a USB to TTL serial cable, and connect directly to pins 0 and 1 on the Yun:
- Pin 0 goes to the receive data connection of the cable
- Pin 1 goes to the transmit data connection of the cable
- Any of the GND pins go the ground connection of the cable
If the cable has a power output pin, leave it disconnected.
Now, you can use the Serial Monitor or some other terminal emulator to connect to the USB adapter. In this case, the speed setting you select in the Serial Monitor's baud rate box will be functional (if you are using a different terminal emulator program, set the speed according to how that program works.) This should let the USB adapter (and your terminal emulator) talk directly to the Linux console. You should be able to set the speed to 250000 when talking to U-Boot, and 115200 when talking to the kernel.
In a normal Arduino, pins 0 and 1 talk to the AVR processor. On a Yun, these pins are also connected to the Linux console port. By running a blank sketch, the AVR processor is ignoring those pins, and you can use those pins to talk to Linux. Just keep in mind that the Tx/Rx polarity of these pins is in relation to the AVR processor - they will be reversed on the Linux side: use pin 0 to listen to the Linux console, and pin 1 to talk to it. (I hope I didn't just get that backwards!)