To be honest it sounds like you have loose or faulty ports or posts. I would shut the unit down,discharge static,pull everything apart except the HDD,SSD,DISC DRIVE,CPU,GPU and remount everything slowly as to recheck every connection for looseness or frayed wires. Look for wobbly posts. When you have problems such as in your description, it,in most cases, comes down to faulty hardware or loose connections that can be recrimped if you have the dexterity to do so. Just remember, the hardware is truly not complex. Its getting simpler every day to build or fix a rig. Everything is generally labeled and you can order new USB ports and wires. Process of elimination!! Pen and paper!! Oh yeah and coffee. Good luck!