That's why I don't have male cats. However, Feliway works very nicely in keeping the calm in a lot of cases.
You've removed the pan upstairs and only have one downstairs and are unhappy that he's peeing upstairs now, well I think the spike mats are keeping him from using the one downstairs, so where is he supposed to go. You definitely need to keep 2 boxes and I would definitely lock him in one room with one box for awhile and have Weebles have access to the other one only. Also if he's peeing on carpeting or near where the box was, put a bowl of dry food right over where he pee'd. They don't usually pee where they eat. My male cat used to pee behind the TV until I started putting a small bowl of food wherever he pee'd and it eventually stopped.
He needs to be segregated from the others, it's too bad but sometimes it's necessary or he needs to start going outside like the others, that will also give Weebles some quiet time from being tortured.
I am having that problem now, my older cat is being tortured by the new younger cat (both females) however the older cat goes outside and is able to have some peace and quiet while the newer kitty is an indoor only. They share two litter boxes and have figured out that you pee in one and poop in the other, it's amazing that the new kitty figured this out almost immediately.
I'm almost thankful that my male cat is gone, they are too big of a pain when they are with other cats. That's why I like females better.