IDE no longer works after preferences JSON add for ESP8266

Had not noticed you were using a proxy.
Use VPN's myself with no issues.

Yes please include some verbose output.

Did you run 1.6.4 from an UNZIP location (not installed) ?

Also what sort of clean up have you been doing after an un-install of an IDE ?
Just using the regular uninstaller leaves a folder behind in one of two locations depending on the IDE installed.

Look up some of "pert" posts he often mentions them and they often fix issues.

EDIT here are the locations I got from Pert.

On Windows:
Arduino IDE 1.6.5r5 and previous:
C:\Users(username)\AppData\Roaming\Arduino15
Arduino IDE 1.6.6 and later:
C:\Users(username)\AppData\Local\Arduino15

I also move my sketches location away from my documents folder as I hav had a couple of issues in the past.

I also use CCLEANER after an uninstall then WISE registry cleaner as well to dig out any remnants of a past IDE