A couple of things not mentioned so far is the fact that the majority of hydraulic filters on a hydraulic system, filter on the return as the filters cannot handle full system pressure.
Transmission filters are different as you are not talking about 2000 lbs of pressure.
Most systems will have a screen on the intake to the pump to prevent large pieces from the sump getting to the pump.
Get a schematic of your system so you know what is involved/included within the system, get to know your system, always check the simplest thing first, always, no exceptions.
if you fail anything in your system you will probably contaminate the entire system, this means you disassemble every hose, cylinder, valve in your system, if you do not, you will recontaminate the entire system and have ongoing problems until you clean the entire system.
The reason manufactures install filters upside down is so you can not prefill, does that tell you something, just because oil is new does not mean it’s clean, do not prefill oil or fuel filters as this is bypassing the filter, just like putting dirty oil or fuel in your engine or transmission. Price out an injector for your engine, want to change them because you pre-filled the filter?