Kool stops squeal something nasty when new, especially on a new rim, toe-in is necessary but X-treem turbo toe-in like what it might have taken to shut them up will be less necessary once they wear a little, which will help with the stopping power.
Creaky saddles are usually from loose clamp bolts, and many creaks that sound like other stuff are actually the saddle or the chainring bolts.
The 25.4 stem will fit all risers. I kind of hate risers for no good reason, and I don't ride them because I ride long distances, but tons of people love them. I always thought this bike was so amazingly old school and beachy that it should have some kind of cruiserish bar with white grips, skinwall tires, and a black brooks. I did white tape on mine, which looked great for the 5 minutes it was clean.