I recently had a Crosscheck built up for me for very similar purposes--just wanted a nice all-around bike. Found a lightly used frame, used bars, and bought the rest--some from the shop, some on-line. I knew I wanted a triple up front, different bars set pretty high, and was trying to get the bike as light as was reasonably possible. I was hoping to spend around $1000. This is my first "nice" bike.
I am actually a little embarassed to say the bike has wound up costing around $1500 (I've paid for it by selling a bunch of stuff on e-bay, but still...) I am happy with the bike--I got to choose every bit of it, from the overpriced but very nice Jones H-bar to Panaracer Pasela tires. Despite my careful shopping the bike still weighs ~25 lbs. I went with mostly XT drivetrain, Bontrager Select wheels, MKS Touring lite pedals, etc. and just put an Old Man Mountain White Rock rack on it. I don't think I could have gotten a nicer bike for the money spent (and if I could have, keep it to yourself
) My only possible regret is the gearing is a little low (22-32-46 & 11-34), but I more often wished for a lower gear than a higher one on my old bike--even more so with a load of groceries (and coasting downhill is far better to me than having to walk up one.)
I guess the upshot of all this is agreeing with most of the other folks--building up a bike almost always costs more than a pre-built (and perhaps inevitably more than what one intends), but you get what you want. I asked around about the Crosscheck complete (the pre-built one) and several people said the components were fine, but nothing too nice. So, as others have said, if cost is the prime consideration go with the stock build, but I think you could rapidly raise that cost by swapping out bars and drivetrain bits so that a custom build isn't that much more.
In general, I don't think you can go wrong with the Crosscheck as long as you accept it as a compromise bike--not as light or fast as a true road racer, shorter chainstays (my heels clip my panniers a bit) and higher BB than a dedicated tourer, but for an all-around bike at a reasonable price the Crosscheck seems great to me.
Good luck and tell us what happens.