First off, here is a string on another website that could give you some more info: Rafts, rafts, and rafts... (fishing) - Mountain Buzz
As I stated in that string on Mountain Buzz, I have a 12' NRS Otter and a 15' NRS Otter and I can rig them for both fishing and whitewater. I like the NRS frames because of their flexibility and the options you have for reconfiguring the bays in different ways for different uses.
12' NRS raft
15' NRS raft
That being said, I fished with some friends who just got a DRE San Juan frame on a DRE 13' raft last fall, and that is a great fishing set up. The ability for both people fishing to stand and cast is awesome, although it is a little cumbersome to cast almost directly over top of the rower/captain for the person in the back. Based on this experience, I am putting a NRS casting floor and custom lean bar in the front of my 15' raft for fishing in 2013 - my hope is for something that looks like the DRE San Juan in the front when I am done.
One pitfall of the San Juan frame is the weight. I don't know the specs, but that thing on top of a 13' DRE raft was very heavy. One word of caution about putting that frame on a Puma series raft is that the Puma's are cut narrow. Again I don't know the exact specs, but in general I think the Puma's are cut around 6'' to 12" narrower than their NRS, Hyside, or other similar length counterparts. With that much weight on a narrower raft, it could get a little tippy side to side.
As for rafts, I prefer hypalon and have been very happy with the NRS Otter series. As one previous post said, most any raft will do fine if you are not a commercial outfitter putting in 100+ days a year on the water. Rocky Mountain Rafts is developing a good reputation for recreational use, and their prices for brand new rubber are very reasonable. You can find lots of used rubber on the Mountain Buzz swap page, and used frames show up from time to time too. My friends got their San Juan frame and oars used for about $2500, and got their DRE 13' raft used for about $2000, so their total package was just under five large after they added some other necessary items. It takes a while to find good quality used rubber, but it is out there to be had.
And final suggestions: make sure to include a trailer into your project budget. IMO it is a pain in the arse to take apart your frame (especially fishing frames) and roll your raft before and after each float, so get a utility trailer to leave it set up and ready to go all summer long. also search around the Mountain Buzz website for other strings on rafts and fishing, there is a lot of info there from experienced rafters but generally with more of a whitewater focus (some that fish too, like me).
greenback: if you are on the front range of Colorado and want some time on a raft before pulling the trigger, shoot me a PM. i can let you row for me anytime you want on the easy stretches of the Upper Colorado, and i will even get on the sticks to let you fish too. sounds like you have some experience rowing a drift boat in your past, so rowing a raft should be no problem for you. have fun with your research.