Today, with Johannes' help, I cleaned the fiber tips of the photodiodes. The effect of the cleaning was dramatic - see Attachments #1-4, which are X Beat PD, axial illumination, X Beat PD, oblique illumination, Y beat PD, axial illumination, Y beat PD, oblique illumination. They look much cleaner now, and the feature that looked like a scratch has vanished.

The cleaning procedure followed was:

• Blow clean air over the fiber tip
• First, we tried cleaning with the Q-tip like tool, but the results weren't great. The way to use it is to dip the tip in the cleaning solvent for a few seconds, hold the tip to the fiber taking into account the angled cut, and apply 10 gentle quarter turns.
• Next, we tried cleaning with the wipes. We peeled out an approximately 5" section of the wipe, and laid it out on the table. We then applied cleaning solvent liberally on the central area where we were sure we hadn't touched the wipe. Then you just drag the fiber tip along the soaked part of the wipe. If you get the angle exactly right, the fiber glides smoothly along the surface, but if you are a little misaligned, you get a scratchy sensation. 
• Blow dry and inspect.

I will repeat this procedure for all fiber connections once I start putting the box back together - I'm almost done with the new box, just waiting on some hardware to arrive.