The front differential is tucked up under there, but if you're up to it you can drop it down a few inches to compensate for your lift. You just have to watch the exhaust routing.
The high-flow pumps are nice, I have a Flo-Kooler in both the Eagle and Pacer. It's a different design but a similar idea.
Ever since owning the Pontiac I've understood the difference a good pump makes; their V8s are really sensitive to flow. The stamped steel like we have always make them overheat, and you really need a cast impeller, it looks like that Hesco impeller, that hasn't had the fins machined away at the edges.
On the stock AMC pumps, look at the gap between the impeller and the body on the pump. If the gap is more then .060 it's just wasting power. I've seen cheap aftermarket pumps have over 1/8" (.125) of gap. It's not something that you notice on the highway, but stopped in traffic on a hot day that gap can make your car overheat. It can also make your pump rub against the sleeve on cylinder 1.