This paper presents a novel method for the modal system identification of a large mechanical structure by combining results from simulations and physical measurements. Specifically, reconstruction of mode shapes was accomplished by comparing simulated and measured amplitude ratios generated using a Nyquist analysis. The methodology developed in this paper improves upon traditional techniques by allowing for statistically cross-referencing relatively few sensor measurements and a relatively simple simulation model. This methodology was used to identify three major modal frequencies and mode shapes of the main aluminum honeycomb sandwich panel gondola structure of the balloon-borne imaging testbed (BIT). BIT was a stratospheric ballooning project for astronomy that was launched on September 18, 2015, from Timmins, Ontario, Canada. Ensuring that structural vibrations do not adversely affect the pointing accuracy of the on-board telescope is crucial to the success of the project. This paper also highlights some of the advantages and drawbacks of the presented methodology and suggests improvements for future applications in balloon-borne experiments. (C) 2016 American Society of Civil Engineers.