Best practice for econometric system dynamics models

Within a project on food security I happened to model Ghana‘s whole economy finding it hard to initialize (initial values of stocks) the model that of course considered a lot feedback loops. I understand that this wouldn‘t be a challenge for general equilibrium models that in turn struggle to feature feedback loops. My solution was slow and dirty letting the model run with fairly high initial values to approximate the initial values that result in an equilibrium. Also relevant I assume is the fact that these kind of models have necessary system boundaries so they couldn‘t simply be based on data on jobs, demand and income (data for Ghana isn‘t complete anyway).
So, does anybody know papers or books dealing with this challenge?