Nevermind, I just realized I did a stupid thing. Instead of making the SKSE64 directory SKSE64<Scripts, SKSE, I accidentally put the scripts folder inside the SKSE. Its working now.
I followed the guide through the entire thing and when I load up skyrim through the SKSE launcher, it works. I can load a new game and it doesnt crash. But when I load the new game I get 2 popups that morehud and skyui can not detect SKSE and wont run. I even ran the getskseversion command and it shows its running. Is this normal? Should I ignore it?