Just did this EXACT swap. The writeup is at my web site:
in the tech section.
Basically, for a YJ you want an 86+ wagoneer - that will give you dana 44 front and rear, driver's side drop, usually no vacuum disconnect. earlier versions had the amc 20, and really early versions had d44s but passenger side drops. 86+ should get you what you want. The only thing to watch for is the vacuum disconnect - you don't want it, and I'm not sure what years/options had them. Make sure you do NOT get quadratrack axles, as the rear pinion is offset to one side on these axles, and yo don't want that.
the 86 gw I got mine from had d44 front and rear, 30 spline axles (1.31 inches?), both normal rotation gear sets, 6 bolt rims, 1/2 ton internal splined hubs, etc etc The waggy axles are nice because they have stronger knuckles and hubs than say a scout axle and the tie rod is already on top of the knuckles. The tie rod and drag link are also bigger and stronger than a YJ, so make sure you grab those and use them.
Get warn premium hubs - my opinion. Gears - lotsa places, I got mine from Drive Train Direct, but there are a number of outlets with more or less the same price, just make sure you are getting high quality american made gears, not cheap italian stuff.
The biggest problem you will face is getting the steering linkage to work, because the location of the steering box, pitman arm length, and tie rod location are all different on a GW. There are various ways to go about it, what I did was move the drag link to the other side of the tie rod and use the waggy pitman arm. If you can grab the waggy pitman arm at the same time as the front axle and steering linkages, that would be a big bonus and may potentially make your life a lot easier. I was staying SUA at the time I did my swap, if you are SOA or going SOA at time of swap that changes things a little.
Anyway, check out the details on the web site and email me if you need more info.