B-17s never bombed at 36k. They could barely break 30 with any kind of bombload, and that was pushing it. To have any bomber flying at 36k as smooth as glass is retarded.
I'd like to see bombers squirrel around, and fishtail pretty badly at alts like that. They were almost impossible to hold steady. B-24 pilots couldn't even fly at 30k, because the risk of them flipping on their back without warning was very high. They couldn't hold formations, either. They had to loosen up drastically because they were all fighting their planes so hard they would ram into somebody else and take out a whole formation.
Solution isn't necessarily wind, or clouds. It's add in the problems inherrent with flying that high: Make the drones scatter so the bombs don't hit the same aim point (more for carpet bombing than hitting a hangar or anything), and make them dip, bob, and fishtail even when on autopilot. Kind of like the squirrely nature of the G4M Betty when you adjust its heading while on autopilot.