I think where the SS kit lacks in cooling efficiency due to a smaller core, a larger radiator will compensate a bit for this.
Since I installed ZZPs redesigned FMHE, I've definately noticed a difference in temp readings and the like.
As far as pump placement, the flojet is self-priming so you can really mount it anywhere. Most people mount them at the bottom of the system but theoretically, anywhere should be fine.
And to save a little stress, mount the pump after the HE. That way the pump isn't being hit it heat-loaded exhaust water from the core.