Everything starts at the drawing board. Engines make a lot of heat, and proven cooling system designs have been around for a very long time, so why not start there? You have a radiator in the front with a fan, so carefully direct that air through a tunnel and around the hottest parts of the engine.
Lets not forget that these are off-road machines, subject to being used and abused in a wide variety of conditions, including water and especially mud. Everyone knows that water and engines don't mix, so the air intake should be as high as possible, and certainly not low in the front, where it could act as a water scoop. Simply move the bed back a couple of inches, or reduce the reclined front seats a bit, and put the air intake behind the front seats, either in the center, or off to each side. The air filter box could be relocated under the drivers seat, affording very easy access, but it must be absolutely water tight.
And remove all that plastic crap covering the engine, which only serves to trap heat. As for the 1000-3 v/s the 1000-5, simply incorporate the 1000-5 floor into the bed, where it should have been in the first place. The bed may need to be moved back slightly, but it would also help the dump angle, so it's a win-win.
See, with a few carefully chosen design considerations, the cost of manufacturing can actually be reduced, while the machine itself becomes much more suited to it's intended purpose.