I disabled SIP and removed System Python. Now Xcode won't let me export apps
The reason that version is protected by Sip is because it is essential for your system to work. Out of all the python you can remove, that one is not on the list.
Normally python is relatively local, as in, everything lives in a single directory, but just replacing a couple files from the brew install to the OS install are not very likely to give you a working version of Python.
The rest you must have installed yourself.

I'd say restore your MacOS and then use brew to install the additional versions you need. Even 2.7, as the OS one is not very good for anything but the OS itself. 
Same as you shouldn't pip install stuff globally but always in a virtual environment so that you don't get dependency crap with OS required items, or worse, OS items that fail to function due to broken dependencies.

Sorry, not the answer your looking for I'm sure, but the best I can give.