In the early diffusion system identification theory by the author, for example in a multi-zonal air flow rates measurement, the constraint equations such as airflow rate balance had been embedded into the tracer gas mass flow balance equations. However, to impose non-negativity on the parameters to be estimated, the regression equation was modified by coupling these constraint equations in parallel to the gas mass flow balance equation. To evaluate the uncertainty statistically, a ratio of index discrepancy from the modeling premises was devised. However, contributions to the least squares from these two coupled regression equations have different magnitudes because of the different physical units, and produces an unfavorable effect on the identification precision. Therefore, to realize an unbiased estimate, the author introduced a set of weighting matrices. These improvements were verified by applying the theory to a case study that performed simulated measurements of the building heat loss coefficient and air infiltration performance.