It is very difficult to help somebody who lack a very basic understanding of electricity and electrical wiring principles. I think you are better off if you contact someone locally who can help you out with this, but some words of warning:
Regarding your question 2:
Do NOT under any circumstances connect the GND on DC side with the protective earth (PE), which I believe you wrongly call "GREEN AC ground". That would be purely hazardous and very dangerous, not only for your equipment but also for yourself. Protective earth is NOT the same as GND.
Your question 1 is not possible to answer without more information because it depends on what the 5V and the 48V is used for.
Your question 3 is not possible to answer without more information because it depends on your BoB. If it is made for using an external 5V than it is better if you don't connect it to your PC USB port. Remember that not all PCs have 5V on the USB, some have only 3.3V.
Your question 4 is easy to answer. EMI filter is always a good idea and can never do harm, only good. An EMI filter is normally connected to your mains input, after the mains switch, before the power supply. Here is a picture of how mine looks like.
Why are you rewiring your system without knowing what you are doing? Are you just guessing that it will solve your problems? Many things can cause noise, and it is not clear if you mean electrical noise, which you can't know anything about unless you measured, or noise generated by your motors which actually can come from a faulty driver or just a simple lose wire. Start with fault analysis because rewiring may result in a lot of time and money spent without real benefit. OK, it may solve your problem because in that process you will tighten the right screws, or change a partially broken wire, but it would be cheaper and quicker to just identify the problems first because you might find the faulty wire or contact and could fix that without changing everything else around. In the end, if it turns out to be a motor or a driver, the whole work may have just been wasted money and time. For all we know, it may even be your PC which is causing the problem, with noise like symptoms.