TwilitlordA couple things: configs should actually still work in tf/cfg, that's where I've been editing mine and they work fine. They rolled over there too. Maps are better put into tf/maps so that they show up in the dropdown menu for a local match (if you still use the menu command and not the console, I guess).
+1
At first I created custom/mystuff/cfg but then I realized that steampipe moved my old cfg into the new tf/cfg location. So I deleted the cfg in /custom and I just use the /tf/cfg and everything works fine.