Anglo,
The whole idea behind Kart using the 'raised pads' was to simplify the process of fitting upper lugs to the slide. It's thought to be easier than fitting conventional lugs along their entire radius. Fitting the hood is really no biggie as long as you take your time, keep your edges square, and remove equal amounts from each side until you hit the sweet spot. Your Kimber should have a conventional, as opposed to a ramped, barrel. The good folks at Kart have a lot of experience at walking people through this and I'd say it's well worth your quarter, to give 'em a call.
Here's how one fella went about it, complete with pics. Hope it is helpful.
Regarding your OEM barrel- I know some got out that had a visible 'wavy' looking defect when examining the bore; Kimber told several folks that these barrels were 'OK' and would shoot fine, regardless. I'm just curious if the barrel you're having the problem with was one of those.