Hi Sean,
Apologies for taking so long to get back to you on this. I think what you are trying to accomplish is less for multiple overimputation. What moPrep is trying to do here is use the variance of the mismeasured observations relative to the variance of the gold standard observations. But if all of your mismeasured observations have 0 variance (since they are all 0!) then this strategy won't work. Thus, you can do one of two things:
1) Provide a standard error of the measurement error for those observations (using the
error.sd argument)
2) Simply set those observations to NA and impute those observations like usual in amelia() (possibly with bounds argument to make sure they will be positive)
Hope that helps!
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University