That timing file looks okay to me, given what you have said
about it. So in run 1, all of the stimuli were in the first
half of that run. And in run 2, all of them were in the last
half.

The 331..560 times look good. Every stimulus time should be
between 0 and 600, since that file has one run per line. So
yes, I think you read the intention of my comment correctly.

My comment about using a 1200 line file would be to generate
the output in one make_stim_times.py command, instead of using
2 and concatenating the results. Either way should be correct.
What you are doing is fine, but just seems to be a little more
work than is necessary.

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One other thing that I see is that your stimuli are actually in
pairs. Did you actually present pairs of stimuli that were 1
second apart, or was it a single stimulus that lasted 2 seconds?

- rick