Yes you can use the Waggie power box. It bolts right up.
Adding the brakes will take some work but it can be done. Your CJ5 has drums on the front. The Waggie has discs. It woud be a good time to convert to discs. There's a lot to it and I'm not going to go into detail. Go to Yahoo or Google.com and search on CJ disc brake conversions. There are various webpages out there detailing different ways to convert. Personally I like the manual brakes in my '75. Converting them to discs make all the difference in the world. I can lock up 35's no problem.
The tranny in the Waggie is a Turbo 400 and it is bolted to a Quadratrac (most likely). Crawl under it and look at the output to the rear axle. If it's offset towards the passenger side it is Qtrac. This auto will not bolt to your transfer case without an adapter. It is also way too long for a CJ5. You wouldn't have much of a driveshaft. Moving the engine forward is a lot more involved than you woud first think also. Look at your frame where the motor mounts are and you'll get the idea. Moving them forward also moves them up. You really don't want to do that.
There are lots of things that can be done with the Wagoneer parts. You just need to spend some time on search engines and looking at other peoples websites for ideas and techniques. A good place to start for identifying equipment is www.jeeptech.com
. Asking questions here and there on these bulletin boards will never get you the entire picture.