The 3mm dia fiber was easy enough to polish just using some very fine (automotive) grade sandpaper - I think it was 600 or 800 grit. "Lick" the paper first or use a drop or two of water as a lubricant.
I still haven't rebuilt with S/PDIF cable - after I broke the first try and went back to electrically cabled for one strobe (optical for the other), I started to wonder why I went to all the effort just to avoid the electronic cable which worked fine. And since then I also went back and bought a small Ikelite strobe (DS51) so I can use it in TTL mode atop the ball mount and let both Inons trigger optically off it for a 3-strobe solution (and to deal with the unrelated 'viewfinder' issue I have with the SLT-A55*).
Anyway back to the S/PDIF - that fiber might be so small it would be tough to polish, might need to push it thru a small hole in a block of some sort to help hold it orthogonal to the paper to do so. Or if you can use the connector end it should already have a kind of 'lens' attached. I was going to 3d print a mating socket for the cable end at the housing side, and then only cut off the cable for the sensor side.
[* If you're curious, the first generation of Sony SLT's (A33 and A55) had a pretty painful limitation for underwater use that only became apparent to me after my purchase. The electronic viewfinder trys to be 'helpful' by giving you a what you see is what you get view based on settings. Unfortunately, with manually-synced strobes (either fiberoptic coupled using my microflash, since I can't open the onboard flash inside the housing, or Inons cabled to the Ikelite socket which can only fire as manual sync) the camera thinks ISO400, f8-11, 1/160th second in typical underwater lighting is pretty dark, so the viewfinder "helpfully" goes BLACK and you can't see to frame. Using the little DS51 lets me electronically connect using TTL so the camera knows the strobe is there and the viewfinder is nice and bright, accordingly. This bug got fixed in all the later SLT models (A65, A77, etc.) by adding the ability to turn 'off' the "setting effect" so the viewfinder remains somewhat linked to actual ambient light levels regardless of exposure settings. But no firmware update for me...]