And I'm pretty sure I put the template right under <mainpage-endcolumn /> or maybe I was doing it all wrong lol. For now, I didn't put the new templates on the main page since it does not work as intended.
I believe the issue is that you replaces Template:Crl with your footer template. The footer template should be placed below Template:Crl. The main page columns float like infoboxes. So since there is space to the right of the left column, the footer tried to squeeze in there. Template:Clr is a dummy tag which doesn't attempt to squeeze to the side of floating content and thus prevents the content below it from doing so.
Yes, you need something equivalent to the clr template. If you think you might have other uses for the template on the wiki, then just copy it from the other wiki. Otherwise, you can just type something like this right before your footer template.