Its always a good idea to flush the radiator before filling it with coolant. Afaik, tap water would do just fine.
I would suggest that you install the cpu, ram, M.2, and the cpu waterblock/cooler on the mobo before placing it in the case then install everything else. Though it would be fine to go with the mobo into the case first since its a huge case with a lot of space to work with.
I think the airflow is fine. The bottom fans, atleast how they're shown in the photo, would be considered intakes since the air blowing into the case.
About the Pump-Res combo, you can "hang" them above the cable holes on the right, so no need to remove any of the standoffs. The image below could be used as reference.