I do agree with kissuryu that the site could use a little less clutter. I think that kissuryuu had a lot of good suggestions as well. Based on those, I've also come up with a mockup of my own that I feel could help to reduce some of the clutter. Don't ask me how I managed to do this just by messing around with the HTML despite having absolutely no idea what I'm doing. XD

Current

Mockup

A summary of the changes I made:
I do agree that we can limit the sidebars to only having one on either side. (Personally I like the right side, but that's just me.) If you decide to implement sidebar customization like you were planning Rei, there shouldn't be a problem with having only one.
I think we can remove all the icons over the banner, that way we can keep the banner intact. The open/close sidebar button isn't needed because it's redundant if we keep the one sidebar on the right (or left). I've moved the Patreon link to the top right. Any important links in the menu icon can probably be accessed from the drop-down menus up top (or can be added to those if necessary.) And the search icon can be replaced by a simple search bar on the top as well. Though we might also want to add a link to the visual search next to it or something.
I also kind of agree with kissuryuu's suggestion of making the sidebar a darker color to match the header, I think that would flow better.
Also, underneath the ad, instead of having links to random characters, which I'm not sure we need since those links are already in the drop-down menus, we can maybe feature the latest forum posts or something similar instead. This is just what I came up with for now. If anyone has anything they'd like to add, please feel free to keep giving suggestions.

Oh, and maybe the drop down menu that says "Etc" can be changed to say "Community" instead, because I think most of the stuff in that menu applies to that title.

[ Edited Jun 11, 2018 ]