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What if there is one (or more than one) missing value (ie, subject did not respond to certain trial)? Should the 1D file be
3:1.2 10:2.1 16 21:1.1 (no reaction time--RT for time point 16)

No, this is not right. First, the program will not run if the same number of extra values are not "married" to each time value -- it will complain.

Second, I don't think there is an obvious way to impute a value for this missing data. In my opinion, if the subject did not react to a stimulus, then something different happened in that trial in the subject's brain, and so such trials should be broken out into a separate stimulus class -- that is analyzed with a "typical" stimulus response (perhaps 'BLOCK(d)' where d=average of actual responses). By putting such stimuli into a separate class, the data from those intervals won't contaminate the results computed from the "correct" or "typical" trials.