I was able to fix the Uplay/Ubisoft Connect. I had Ubisoft Connect installed seperately via NonSteamLaunchers so i could play through brotherhood.

All i did was going into the steam apps compatdata folder and deleted ubisoft launcher in program files x86 in the revelations C drive, and copy over the ubisoft launcher folder from the custom ubisoft connect that was installed by NonSteamLaunchers.

It didnt work 100% and there probably a better way to do this as the text didnt copy over. everything has placeholder text, but if you know what to press its easy enough to navigate. You also still have to type in your ubisoft password every launch but it works. once in game everything seems perfect.