Tracking the times of the individual sets on D3 helps. When progress is very, very slow, it is easy to perceive it (wrongly) as being stuck. It is likely that your stamina is improving ever so slowly and it takes months to see it in the end result. If you track the timing and the reps in the sets, 1) you can focus on increasing the reps in the first set/second set/... and see the progress 2) you can observe the reduction in the times during or in-between the sets.
If it helps, I have been doing SF for 18 months now and working on Level 4 right now. It took me nearly an year to build up the strength to do the 41 push ups in under two minutes. My projection is that I will take another 6 to 9 months to complete L4 pull ups in under 1m 45 seconds. By end of 2015 summer, I might pass L4 and start a new 18 month journey of working on L5 :)
In short, take it easy, give yourself time, and let it happen.