I hear you about the shorty 4s. I had my LBS remove them after my last squeal fest in the rain when I could barely stop and add travel agents and Tektro RX5s with Kool Stop pads. I'm much happier. The travel agents work pretty well at taking up the cable pull from the STI levers. I would first try Kool Stop pads then if you aren't happy you can go with mini V brakes. I've heard the other Shorty models aren't much better and the Shorty 6 actually squeaks more. Another option that my LBS recommended was the Shimano BR 550. Both the RX5s and the BR550s use cartridge brake pads so they are a little easier to change out.

Looks like you went with the Quatto SL. I'm actually selling my Crank Brothers Quattro SL as well. I find the standard Crank Brothers egg beaters much easier to enter and exit. You might consider those before going Shimano. Looks like a great bike. I'm actually lamenting my double crank at this point and lusting after the Jake's triple. Guess I need to lose another 20 pounds.