So when you came here, you had a comfortable bike. Now you've followed everyone's advice, re-fitted the Velocity and you've got an uncomfortable bike. This is progress? Do yourself a favour and refit the riser stem. As it is shorter than the Velocity, you will get sharper steering with it, and if it gives you a better riding posture than the stretched-out position you have now, then you will ride faster for longer.
The new saddle is an improvement, but you have mounted it as far back as possible, which is making the bike even longer. A size 19 Kona is designed for height range up to 6-3, and you're making it slightly bigger than that with the saddle where it is.
No, there is no reason why you shouldn't get excellent results with V-brakes with that fork. As has been said, you should fit V-levers as well, as you would get very sharp, unmodulated braking with the canti levers. The Fire Mountain was fitted with a triple-butted Project 2 in 1994, so the fork is one of the best bits of the spec.
.
