I think you're misinterpreting autocorrelation. The correlation peak at 5000 is not due to a single location in the time series, but rather to the fact that the entire time series is similar to itself, when offset by 5000 samples. As much of that peak is due to the time series peak at 18000 as it is to the time series peak at 7500. Your autocorrelation will get very strange if, for example, you do not have a truly periodic time series (that is, if the interval between pulses is nonuniform).
If you can isolate one example of your pulse, and choose the location you want as your t=0, then a correlation of that one pulse with the time series will give you just what you want. Each pulse will light up clearly, at the time location at which it occurs. Then you just need a peak finder.