Contrary to the academic interests of other existing studies elsewhere, this study deals with how the alignment algorithms such as sensitivity or Differential Wavefront Sampling (DWS) can be better used under effects from field, compensator positioning and environmental errors unavoidable from the shop-floor alignment work. First, the influences of aforementioned errors to the alignment state estimation was investigated with the algorithms. The environmental error was then found to be the dominant factor influencing the alignment state prediction accuracy. Having understood such relationship between the distorted system wavefront caused by the error sources and the alignment state prediction, we used it for simulated and experimental alignment runs for Infrared Optical System (IROS). The difference between trial alignment runs and experiment was quite close, independent of alignment methods; 6 nm rms for sensitivity method and 13 nm rms for DWS. This demonstrates the practical usefulness and importance of the prior error analysis using the alignment algorithms before the actual alignment runs begin. The error analysis methodology, its application to the actual alignment of IROS and their results are described together with their implications.