My pedals seem to have developed a click, on each pedal stroke my pedals have a weird click sound, and I can feel it, I was thinking maybe it was the bottom bracket? But it only happens when I am clipped in.
You have the old SPD-SL type, what's the wear like on the plastic plates?
You need to replace the plates when they wear otherwise they can cause a bit of clicking sound with the cleat. The newer SPD-SLs have a wider metal plate and don't really wear out.
Looks like the plastic plate has worn right through.
New plates are hard to find, but I'd recommend getting a set of the new 105s with the wider metal bottom plate. Bearings shouldn't have in the pedals this quickly.