1 - did the rig ever work? It is always best to get the stock rig to work before you do any modifications. Since you have already installed the KD8CEC software and it is working do not go back.
2 - Get the Memory Manager software from GitHub: https://github.com/phdlee/ubitx/releases/tag/v1.11 then use it to see where the calibrations are at this point. If you go to the HamsKey.com blog, you should be able to find instructions on how to use the Memory Manager.
Once you have the software up and running, connect it to the ubitx and read the current calibration values in the rig. The calibration value is not so important at this time. The BFO value is. It should be somewhere around 11.0550 MHz. If it is very far from this value (more than 20kHz, then set it to 11.055500 as a starting point and see if the antenna connection changes the received sound.
The microphonic connection could be a cold solder joint on the volume control, a bad volume control (not real likely), a cold solder joint on the board, or the LM386 socket. There have been some reports in the past about cold solder joints on the crystal filters of the board. It the soldering that you did passes inspection, then you could take a good magnifying lens or loupe and verify them. I would suggest you try to isolate the offending part by tapping lightly around the rig to see where the sound is the loudest.
As background, I had this issue with a v4 that I built. It is still there, as far as I know, just overwhelmed by the signal from the RF sections. As Reed suggested, the place to start is to ensure that the BFO is calibrated. Until then, hold off on any major surgery.
Let us know how things progress.