Dynamic testing of systems is most realistic of real-world conditions when multiple input and multiple output (MIMO) techniques are used. To replicate measured environmental conditions, a series of desired outputs (responses) on the system must be realized by inverting the frequency response functions (FRF) matrix for input estimation. System identification is dependent on the number of inputs and outputs, which affect the type of solutions. In input estimation, the auto spectra of the determined inputs are affected by both the auto spectra and cross spectra of the desired outputs. This research evaluates errors and investigates two sources in an experimental setting. The first significant error source is test-to-test variability in FRFs from system identification tests, quantified by magnitude variability from long-duration tests. The second significant error source is the realization of time histories from frequency domain inputs. The spectral content of the realized random process deviates from the desired content and is also quantified. The structure is a linear three-story frame fixed at the base; two inputs are provided uniaxially with the use of suspended electrodynamic shakers. The proposed model for error sources was found to be effective in predicting errors in a SISO (single-input single-output) and a square (2-input 2-output) MIMO test.