For birds, "Birds of Chile" by Alvaro Jaramillo is indeed what you want - excellent, authoritative, and compact.
For mammals and other fauna, there is an inexpensive and compact "Wildlife Guide to Chile" by Sharon Chester that I've seen in shops but have no experience with. Looks like it's still in print and readily available. A more authoritative books on mammals would be "Mammals of the Neotropics, Volume 2: The Southern Cone" though this is more a text and less a field guide. Readily available used for a reasonable price and a good book though a bit bulky for travel. I'm sure there are more books out there but I'm not familiar with them.
The Carretera Austral is just plain awesome, it is one of the most beautiful parts of S America and for me is one of the absolute highlights of my 3+ years of van travel in S America. I don't think there are any real hotspots or unique birding spots and for the most part you should have the same mix of species for the entire trip. Probably the best bird to look for on the trip is Rufous-tailed Hawk. You might be able to find a Patagonian Forest Earthcreeper in more open/drier woodlands; there are few records down there but I think the species is still turning up in new places as people have recordings and can ID it on voice and know to look for it. I recently found one a bit further north than prior records on the Argentine side of the Andes. You will likely see some Steamer Ducks from the ferries, and you will likely get Spectacled Duck along the Carretera itself. Magellanic Woodpecker is guaranteed if you familiarize yourself with the vocalizations ahead of time to track them down. Some other nice birds that come to mind that you should get are Magellanic Penguin, Red-legged Cormorant, Chucao, Black-throated Huet-Huet, and Andean Condor...
Though not on the Carretera Austral proper, be aware that the best known place for Pincoya Storm-Petrel is the Isla Chiloe ferry. If you have a few hours to spare on the Puerto Montt end of the trip you can drive down to the ferry terminal, park, walk on the ferry and ride it back and forth as many times as you like looking for the Storm-Petrel. The ferry is also good for Commerson's Dolphin. It is very inexpensive for pedestrians and they frequently don't even collect the money. I saw numerous dolphins and a couple of Storm-Petrels in one trip, in the rain, though sometimes it can take a few trips, and some people miss it.
Enjoy your trip, it's an amazing area!