The blinks are actually triggered by the bootloader. That blinking you describe doesn't sound like its unusual. If the DTR is pulsed repeatedly that can cause that type of blinking before an upload can begin.
I am using this board on a daily development for months, however, I don't think that I shorted it somewhere because my other moteino's are working perfectly.
In that specific board, I resolder 5-6 different antennas and flash it hundreds of times, so I just want to repair it if it's possible.
That's quite revealing, useful to know.
I am asking if it's possible to find a way to troubleshoot the MCU or check if the bootloader is corrupted.
Maybe the bootloader is corrupted although the protection fuses should prevent that, but perhaps not at non compliant voltages, that could perhaps happen, instructions to jump around and randomly delete something in flash.
If thats the case, then LDO voltage needs to be restored to 3.3v, then the MCU can be ISP checked/reflashed with the bootloader, that's what i'd do.
But not sure its even worth the effort, given the history you mentioned I would move on to another Moteino.
Unless you're very remote somewhere and have nothing else to work with.