Shouldn't you make premake ProxHTTPSProxy with the config.ini, and also a script could be made to do the trusted zone. Also restoreWUXP2003 needs a patch to allow it to work after you already launched it once (batch needs a mod else when you run it second+ time it will not work). And you should also make more updated root certificates.
Also the Certificate Updater 1.6 always fails for me but it works without it