Some interesting things to think about there Matt
Think some of the pumps I've been looking at can lift to 5m! so the engine being about 60mm tall shouldn't represent a problem.
Also, for every unit of water which goes up, a unit will go down and in a sealed system that should mean the pump isn't really having to do a lift, so that just leaves drag through the cores which I wouldn't think would be a problem.
Tis a good point about the anti-freeze though! I'm hoping that if they can live in salty salty sea water then they can cope with pretty much anything....unless the anti-freeze attacks the seals.
I reckon that going for the submersible pump should mean that the pump itself can reject heat into the water.
Did you rig yours so that it pumps from the resevoir, through the rad at the front, up to the cooler and then back to the resevoir? That's what I had in mind, with a small header tank to make sure everything stays full and bubble free.