On the 6s, generally speaking, moving the original home button over to the new screen is enough to keep touch ID working. Problems may occur with 3D touch, but a good quality screen will usually work fine. If not, THEN replacing the back plate will be necessary.
White toothpaste. Don't use whitening, or added baking soda. Spread it on thin, let it dry, buff off with a clean, lint free cloth... Depends on the severity of the scratches. Alternatively, I've had luck with wax pencils that are made specifically for the task, as well as Pam cooking spray.
There are separate mics. The speaker mic is part of the upper main board assembly, while the standard mic is part of the lower charging board assembly. Replacement is easy and inexpensive. Follow the guides on this site. 10 minutes worth of work, if you really take your time.
Use a hairdryer to heat the top of the phone, guitar picks to lift the glass, and the thinnest gage wire you can find to separate the glass from the touch digitizer. Work from top right to bottom, being very cautious of the ribbons under the top left and under the back and menu softkeys. This particular phone has a very high failure rate when separating the glass from the screen. Be prepared to buy a new assembly. You will need LOCA and a UV dryer to adhere the new glass. My store will not replace glass only on any s5 or s6.
The charging port handles all of the issues you just listed. Open the phone again, and disconnect asks reconnect the port assembly connector beside the battery connector. If they doesn't fix the latest issues, order a new port assembly off of eBay. Who is the original carrier for the device, and on which network are you attempting to use it?
This may or may not work, but go into Settings > General and scroll all the way down to reset. In the reset menu, choose reset Network settings. Let the phone do the repair, and reboot. Hopefully this works for you!!