The speeds don't matter for collisions - any time two bases overlap you need to make the pilot checks, and you resolve each speed phase completely before moving to the next. It's entirely possible for a speed-5 plane to move and collide with a speed-4 plane, which then moves and collides with a speed-3 plane, then that speed-3 plane goes on to move and collide with the speed-5 plane - checks would have to be made each time.
After the collision is resolved, assuming both/all of the planes involved are still flying, you keep the bases stacked as best as possible. You may need to set the actual miniatures off to the side if they're really clustered together.
Thanks. That was the ruling we made. I'm glad to hear we were playing correctly.