EDIT: This might not be necessary. Refer to the original post and see updates.
I noitced that the method I described in a previous post does not work on Arch Linux. I came up with this quick (and probably dirty approach) to get the same effect.
First run this command:
xkbcomp $DISPLAY original.xkb
This will dump the current xkb config to a file named original.xkb. Make a copy of this file:
cp original.xkb swapped-alt-ctl.xkb
Edit the newly created swapped-alt-ctl.xkb file. Find the codes for LALT/LCTL and RALT/RCTL and swap them. For example, in my own file I found these for left alt/ctrl:
<LCTL> = 37;
<LALT> = 64;
I changed that to:
<LCTL> = 64;
<LALT> = 37;