The Kona has Deore/XT level components, an MZ-Comp fork and Shimano Mechanical discs. The Rockhopper has Alivio/Deore, an Axel Comp, and Tektro brakes.

No doubt the Kona has a better spec. The Kona has deore with even an XT rear derailleur as opposed to Alivio/Deore/Truvative stuff. Probably worth the extra $$$$ just there!

The forks are about equal as I don't have a lot of faith in either model. The MZ-Comp or the Axel Comp will feel about the same. Not bad forks for the money, just not significantly different levels. A lot of people prefer Marzocchi over Manitou, but the internals of the forks are almost identical.

Brakes. Both cheap! You have cheap Linear pull compared to cheap mechanical discs. Tough decision. I'd almost rather have cheap linear pulls and upgrade to Avid Mechanicals later than starting off with the cheap Shimano's. If the shop would consider swapping out for Avid's at time of purchase, I'd definitely go that route, but I wouldn't spend any more for the Shimano's if all else were equal. (Which it's NOT!)

Regarding everything else???? I like both bikes about the same. A lot less people have Kona's, so that alone would steer me in their direction (I'd rather something out of the norm)

It all boils down to how much can you afford and then the test rides! Actually the test rides first! Then how much.