I can't seem to figure this out.

I'm trying to use my third battle pet (weakest) to fight the newest challenger, but even if I select "choose weapons" it preselects my tier 11 battle pet's set, and when I click customize to try to switch to more appropriate weapons, I can't figure out how to actually do that.

"Equip weapons by clicking them in the lower box and arranging them for battle in the upper box."

There are 8 weapons (the t11 set) selected already. I can only move them around and clicking them does nothing. If I try to click the other weapons in my armory, it gives an error saying there's already 8 weapons. How do I unselect this battle set or choose my own weapons before battle? What am I missing? Do I just have to delete one of my 3 battle sets and make a new one to make this possible?

Okay so after you click the "choose weapons" option, go to the "customize" tab like you did. But instead of clicking the 8 weapons listed at the top, you need to do the selecting and unselecting in the scroll box just below that. You should see all of the weapons in your armory in that box, the ones you have selected will be grayed out/transparent-ish and all other weapons will be in normal color.

Click the grayed out ones that you want to un-select and then click the ones you want to choose for the battle. You have to remove the ones you don't want before you choose the new ones. I hope this makes enough sense.

OH! I see that now. The preselected 8 are grayed out in the bottom scroll box so I click those to unselect them. I feel like a fool, lol. Thank you!

No problem, it is a bit confusing. Glad I could help :)

Depending on how many times you want to fight the new Challenger, it might be worthwhile in terms of RL time-savings and aggravation to either re-create one of your battlesets just for your weakest pet, or waiting until your weakest pet can handle one of your stronger battlesets.