Back in 2009, my wife and I aimed to hit every brewery in Colorado (at the time, not including duplicates, there were 104). I'm at 83 and have a little catching up to do with all of the smaller breweries popping up. Not sure how many you plan on hitting in a day (my record is 7 in one day... and yes, the wife was driving), but here are my suggestions for the south route:
If you're taking 191 south out of Moab through Cortez to Pagosa Springs, be sure to stop at:
1. Main Street Brewing in Cortez
2. Ska, Durango Brewing, and Steamworks in the Durango area
3. Pagosa Brewing and Pagosa Pub Works (haven't been to PPW) in Pagosa Springs. Pagosa Brewing has a coconut porter that is amazing -- almost always "sells out" at GABF...
4. Three Barrel Brewing in Del Norte -- this is possibly my favorite brewery in Colorado and practically no one knows about it. We stopped by on a Thursday afternoon to find the brewery run by John Bricker out of the back of his insurance agency (the cold room literally separated the insurance business from the brewhouse!). Be sure to call ahead -- it looks like they may be running a brewpub now, but it's been a couple of years since I've been there. If they're not open when you're passing through, you can always stop at Farrago Markets Cafe in Pagosa Springs and get a sandwich and some Three Barrel Beer.
5. San Luis Valley Brewing -- nice brewpub in the middle of downtown Alamosa.
Those are the high points I can speak to in Southern Colorado. If you're going to go back to Grand Junction and drop in through Telluride, you've got:
1. Kannah Creek and Rockslide in Grand Junction, Palisade Brewing in Palisade (sister city of GJ) -- there's also a decent micro distillery pretty much in the parking lot of Palisade Brewing. Depending upon when you're going, Palisade has some great peach orchards you should check out. There's also a number of wineries in Palisade, but don't expect Napa.
2. Horsefly Brewing in Montrose
3. Colorado Boy in Ridgway
4. Smugglers in Telluride
5. Ouray Brewing and Ourayle House in Ouray
6. Silverton Brewing in Silverton
7. Then on to Durango.
As far as places to stay are concerned, I would highly recommend checking out VRBO. My wife and I are taking a class from Tom at Colorado Boy in October and found a great apartment in downtown Ridgway for a very reasonable rate. Traveling south from Grand Junction to Durango will take a good chunk of the day, especially if your plan is to go through Telluride. Let me know if you have any questions on the other breweries in the Denver area.
Just a minor correction on Crooked Stave: they're currently an alt-prop (I believe) with Funkwerks in the old Fort Collins Brewery location (Fort Collins built a new brewery a few blocks away and FW/CS moved in). Hop you enjoy the trip – Cheers!