We present an approach to upgrading the beam transport system at the Navy Precision Optical Interferometer. These upgrades together will provide consistent beam transport, improve fringe contrast by preserving beam wavefront, reduce tracking errors by increasing the frequency response of the tracker, and automatically realign the entire transport train after thermal drift over the course of nightly observations. The beam transport system passively redirects stellar light from the telescope output to the fast delay line through a train of flat mirrors. This multi-mirror transport train reduces wavefront preservation due to stack-up of surface flatness errors. We demonstrated previously by using a contour-conformable mirror instead of one of the flats in the train that a 63% improvement in wavefront flatness is achievable. Also, the 25 Hz tracker is replaced by a 100 Hz tracker to further stabilize the trajectory during observations. Finally, we include an auto-aligner to systematically realign the entire beam transport system from thermal drifts. This is necessary for long baseline interferometry with short drift time constants. The beam transport system is common to all front ends (telescopes and siderostats), beam delay, and back-ends (beam combiners and detectors). These three upgrades expand the utility of the NPOI from a relatively short 97 m baseline interferometer to its full reconfigurable 437 m baselines and allow consistent beam transport with various potential experimental telescope front ends and beam combiner back-ends. In this paper, we describe our three-pronged upgrade approach, experimental method and results, and recommendations.