Zeldo's Additional Pipes has the Advanced Wooden Pipe which will take out only the item that you have in the filter. Chuck an empty bucket in the filter and that will be only item that gets pulled out.
His mod also has the Advanced Insertion Pipe which will instantly insert the item if there is a space available otherwise it will keep going.
Also contains the teleport pipes. This would allow you to teleport your buckets in rather than keeping the setup near the reactor = more space.
I think in the latest one there is also a redstone pipe that sends out a redstone signal when an item passes through it.
Give it a look, although the latest release is for BC 2.2.3 while the latest Buildcraft is at 2.2.4. Zeldo updates like a madman though so it won't be long.