Just to get things straight in my head, is the psu fan an intake? If so I guess I could leave the hard drive bay in place as this would shield the psu from its airflow.
It is meant to exhaust air from the case and the PSU, so it is an exhaust fan by design and function (technically, it is also the PSU's intake fan). The fan still has an intake side and an exhaust side, i.e. input and output, a.k.a. pull and push.
Since the expected load is so small, both PSUs would more than likely run about as hot or cool. It's not the worst investment in the world, but it is serious overkill.
Ducting isn't a bad idea, but it shouldn't be necessary here. Diminishing gains and all that. I think the confusion is the result of the wonky airflow setup... in fact, I don't see any reason not to tell Lian Li to shove it and wire the fans up in the regular pattern. The HDDs would have fresh air, you could put the cooler fan on the right way around and all would be well. Wouldn't even need the top vent for anything.
Tape sounds like a good idea to keep out dust. Hope the case comes with a vent cover for the top too.
PS. SCRATCH THAT. Because of the stupidity that is the Lian Li PSU placement in this case, you would have it blow its hot exhaust straight into the intake at the HDDs. God is this thing dumb. Just go with the standard setup and hope for the best.