Hi Maureen,
It is not unusual to have more shocks than observed variables, see e.g. Smets/Wouters (2007), AER.
As with any statistical problem, there is no problem with a parameter being "insignificant" as you called it. It simply means that your parameter is not statistically significant from 0. And without prior knowledge of this parameter value, you cannot exclude 0 as opposed to any other value.
If it is extremely unlikely that your parameter is 0 in the population (e.g. the coefficient of relative risk aversion is estinated to be 0), this means you already have some prior knowledge about that parameter (not 0). In this case, use Bayesian estimation with an informative prior that excludes the 0.
If you already did Bayesian estimation with a prior that did not exclude 0, compare the posterior with the prior in order to find out, if the data is really uninformative due to the missing series as you claimed. If your parameter is estimated to be 0 with a high precision due to the likelihood, the unobserved data is maybe not your problem. Probably, the parameter is truly 0.[/list]
Best
Johannes