Does anyone know of any resources for the processes that go into cleaning out a newly fabricated hydraulic reservoir? Anybody in the field that can share their experience or company procedures? Just looking to better understand and implement these sorts of processes into my company's routine.

While specific flushing procedures vary with each company and with each component or assembly, Job Responsibility 3 of the Mechanic study manuals give general guidelines for cleaning and flushing systems.  ISO 23309 also gives guidelines for flushing assemblies and machines.

For cleaning new hydraulic reservoirs, people usually go for solvent flushing or high-pressure washing. Have you looked into industry standards like ISO 4406 or NAS 1638 fnaf yet?