Having just diagnosed a tail/brake light situation I can maybe offer a little help.
First and foremost, make sure you have good grounds on all the light sockets and that you have the right bulbs in there. But it sounds like you might since everything else is working. Also make sure you have clean fuse connections. Sounds like you might have all that covered.
My problem was intermittent tail/stop light functionality and it was due to bad fuse holders. But in trouble shooting I stared at the wiring diagram a lot.
It looks like the brake switch has a connection through the directional switch in the steering column. I think that might be your issue. Fortunately I didn't have to tear into my steering column wiring but it sounds like you might have to find that connection and see what's up.
I think the way it works is when you step on your brakes, you send power to both left and right brake light bulb elements, which is the same as the directional element. When you turn on either directional, it just interrupts that brake light power using the flasher relay (purple wire)
From the diagram, the brake switch is always hot from the orange wire from the fuse box, and when you step on the brakes it completes the #14 circuit which sends power to the white wire into your steering column. From there is goes to the green & yellow circuit which is stop lights/directional lights (green is right yellow is left). I think maybe you have a switch problem from white/green/yellow/purple in the column. But I've never dug into that switch so I can't offer much advice beyond what the diagram shows.
If you don't have the diagram I can try to pm a pdf to you. I found it on another forum site so I'm not sure its ok to post it.
I'm not an expert by any means, so don't go tearing into the column just yet until you get some other feedback and do some more research. I know its not easy getting into the column wiring.