A search for rare and forbidden decays of the form D+ -> h+(-) l+ l-(+) has been performed, where h is a charged pion or kaon and l is an electron or muon, using 1.5/fb of data that was collected by the LHCb detector during 2016. No statistically significant deviations from the background only hypothesis are observed and upper limits are given for 25 final states, with 23 improving upon the previous world's best measurements. The majority of these limits are improved by more than an order of magnitude and some by up to a factor of 500. Detector alignment studies are presented here that have been used to influence the development of the LHCb Upgrade VELO. This has included the alignment of several thousand testbeam datasets which were then analysed to provide results that guided the design of the new detector. Furthermore, a comprehensive study on the physics impact of thermally induced distortions of LHCb Upgrade VELO modules has been performed. This work resulted in changes to the manufacturing and quality assurance procedure and will help ensure optimal performance of the final detector. This thesis also discusses various efforts that have been made to improve the analysis ecosystem in high energy physics in response to the challenges faced during the aforementioned studies. This includes improving the tools, procedures and software training that are available to analysts to improve productivity and encourage long term analysis preservation. Such improvements will be essential to effectively utilise modern high energy physics experiments which are unprecedented in both scale and duration.