Your config is full of syntax errors.
You have $mod and $alt in a lot of bindings, but do not define what keys $mod and $alt are tied to.
set $Mod Mod4
set $Alt Mod1
which is fine, but then use bindings like:
bindsym $alt+f exec thunar;workspace 3;focus
bindsym $mod+Mod1+Left workspace prev
which aren’t going to work and mess up the window manager.
You will need to use the i3 documentation to go through your config and clean up the syntax.
Also, you’re launching sxhkd (to launch applications?). Make sure there are no keybindings in the base.conf file that conflict with the i3 key bindings. Better still, dump sxhkd and define everything in the i3 config file.
And what is this conky -
exec --no-startup-id conky -c ~/.config/i3/.i3wm-2rc
You trying to run a conky on the i3 desktop? That can be done, but if the conky syntax is off, it can mess up the window manager. Comment out that line when you clean up the i3 syntax. Once i3 is working, try running the conky.