Yes, the A/C raw water circuit should have a through hull w/ a hull grill or strainer, then the seacock, filter and pump, all below the waterline, as the pump will not suck uphill. The run to the AC is fine.
Please, please, please return all of those brass fittings and instead use either bronze or Marelon, both rated for below the waterline. Those shiny brass parts will become brittle and fail.
The seacock does not have a flange and does not have a reinforcement backing plate. As such it does not meet ABYC. The seacock should be strong enough to resist an adult standing on it, exerting sideways stress, expressed in pounds in the spec.
The image shows a reinforcement plate for the transducers.
My guess is if that through hull seacock was installed incorrectly, as shown in the image, I would also suspect that the hull hole is incorrect.
The hull hole should be lined w/ epoxy (not sealant) if the hull is not cored. On a cored hull, the coring should be scooped away and replaced w/ epoxy.