Signal correlation - matching specific points Question: What are some recommended techniques for matching specific patterns in data sets?
Background
I have several thousand sites for which I have collected time series data. In the example image below we have increasing time in y-direction with data streams from 2 different instruments shown from two sites. I have added hand-picked, color-coded correlation markers for four significant events.  Normally we would pick 10-15 of these markers at each measurement location.
Typically, these markers are correlated by hand, however, with 1000s of sampling sites this is not feasible in a reasonable amount of time.  I have performed hand correlations on ~150 of the data streams, but would prefer to use an automated or semi-automated process to do the correlation.
We have the following beliefs about the data:

By picking a sparse data set (e.g., the first 150 hand picked correlations) we can make a strong guess about the location of the marker in adjacent sites.
The time-separation between markers is not constant, but has only minor variation
Marker A will always come before Marker B, and Marker B before Marker C and so on.
Not all markers will be present at all measurement sites
Not all measurement sites were able to evaluate a full time series (in example below, imagine if one had been cut off at 8000ms instead of going past 10,000ms
The data can easily be normalized to have a similar range of values.

Prior Approach
I have used both DTW and Fast DTW (dynamic time warping) to perform the task, but it only works well when there is a full and complete data stream and when all markers are present.  The downside to DTW is that it is an O(N2) approach, and with data streams of 20,000+ samples and about 5000 measurement sites, it is simply too computationally slow.
Restatement of Question

What are some recommended techniques for matching specific &quot;markers&quot;
in time series data?
Are there techniques that just evaluate certain
portions of the data stream vs. something like dynamic time warping
that evaluates the whole data stream?
What data pre-processing should
I consider to make this computationally easier?

Example Data
I'm no expert with signal processing but my first attempt to solve the complexity issue would be to downsample the time series. For instance if you resample a 10k points series to say 100 points, methods such as DTW can be applied to get a first approximation of the &quot;global&quot; similarity between 2 signals. This would take much less time than comparing the full time series, and then based on the result (for instance using a threshold) only the pairs of signals with high similarity would be compared fully. In other words, the first step acts as a filter so that only a subset of the pairs need a detailed comparison.