Definitely get CRC
(the bible) and/or WWSR
(the new testament). I like CRC a little bit better. I feel like the maps and put in/take out info is a little better, but WWSR has more content outside of Colorado. They are both really good, and I think most people who live in Colorado own both.
I wouldn't set up a permanent base anywhere. You can cover a fair amount of terrirtory and hit a lot of quality runs in a week. Assuming you have a couple days travel time so only have 5 days to boat, you could do something like this:
Put in at Pinnacle rock, run Parkdale (III) and the Royal Gorge (III/IV). The hardest rapid in the Gorge is probably Sunshine, which is an easy scout/portage river right. Drive up to Salida to the play park if you have extra time.
Numbers (IV) + Fractions(III). Hit the Buena Vista play park after. There's a trailer next to CKS (kayak store in BV) that sells really good burgers. There's a Quincy's in both Leadville and Buena Vista. I've only been to the one in Leadville, but you get a good steak dinner for $9.
Take 24 over Tenessee pass and hit Dowd Chute (IV). Drive east and run Clear Creek from Lawson to Idaho Springs (III+), then Lower Clear Creek(III) down to the Golden play park. You could do Upper Clear Creek(IV/IV+) instead of Lower if you were comfortable on Numbers.
Drive up to Fort Collins and run Steven's Gulch through Bridges take out (Upper Mish, Lower Mish, Poudre Park, and Bridges runs - all mostly III with 2-3 class IV rapids). Can surf legend wave at bridges take out or run your favorite section again if you have extra time.
Run Upper Rustic(III with one IV at the start you can skip) and Lower Rustic(III+). All colorado water is cold, but for some reason the Rustic sections on the poudre always seem extra frigid. I usually bring hot chocolate.
That's focusing on whitewater with easy shuttles. All those runs the shuttle can be biked or hitchhiked, and almost all of them are roadside so if someone gets freaked out it's easy to get out. Unlike out east, there's plenty of public land out here if you wanted to camp (except on the front range). If not, you shouldn't have much trouble finding hotels wherever you happen to end up for the day.
I think the Ark and the Poudre are the two best rivers in the state for the number and quality of class III/IV runs. Hit them both if you can, but if not the Ark is more central with more to do around it.