The speed doesn't need to be exactly 50%. I'd helped another on my server to build one and he was getting dark matter at a little below 50%. 50% was just the number I'd originally read somewhere, so it was my target number and I get dark matter pretty consistently with it.
My colliding area is covered all around except for the bottom. I have the obsidian pipe below the tunnel where the particles collide. I do not believe it'll work if the obsidian is in the way of the particles as theoretically the particles collide with one another.
I will leave my accelerator on for a time, and I notice that it gets out of sync with each other sending particles out at different times. It does not appear to affect getting dark matter. At the time I made my reactor, I also had to have 8 atomic electromagnets per section of tube, as opposed to the 4 per section you have above. I do not know if any of this has changed with the recent patches. I will say you'll probably want a bit more space between your accelerators to put some piping to keep the accelerators running automatically for a bit, but they should work the way they are otherwise.
By the by, if you screw up placing these things and are tired of breaking them with a pick that takes forever per block, try using a mining turtle set to tunnel. Picks them up no problems.
In summation, I'd say drop the obsidian pipe down one and close off the remaining spaces, build your tunnel, and this should work.