I think you are trying to do too many things without knowing why. You say it worked BEFORE you started messing around with brains? In that case it is obvious that the the brains is wrong OR you changed more than just added brains. Go back to that stage, deactivate brains and start over. Noise is NOT the problem if you can control the VFD manually. Once you can control your VFD and spindle with the Mach3 manually you can start experimenting with brains, but make sure you KNOW that the communication is still OK and manual control still works. I would NOT experiment with the voltage level in the PC because that might fry your PC. Have you tried to analyze the actual data which is sent from the PC? I think that the problem is mainly not at the VFD or the receiving end, but the sending. It is very likely that you send rubbish which the VFD does not understand so it is not answering. Get a communication port analyzer and check the data. Get a 5V power supply. A phone charger is very good for this purpose because it gives clear 5V. That is better than manipulating BIOS, I had no idea that you change the voltage level through BIOS, but I think that is not a good idea. Also, what is the problem with uploading video? Just upload to Youtube and place the link into the "Insert Video" here.
Electronics is difficult if you have no knowledge, no instruments and don't know what is what.