Not sure what your plans are-whether to just have something to hit the trails with in more or less stock form, or something you plan to modify, or if you want a Willys to restore. That will influence what you want to look for. If a restoration is in mind, the tub condition will be most important and they all rust in the same places-floor hat sections, sills-especially in the tool box, spare tire hat section, and rear tub mounts being the most common. Also look for frame cracks-most common on the frame horns and at the ends of the front cross member under the radiator but also occur between the rear spring hangers. You usually also get rust through in the center on the rear cross member where it has the reinforcement plate on the inside-great moisture trap.
You can buy just about everything, but a lot of what's available is import and of very questionable quality. You are almost always ahead to rebuild the stock parts or find replacement stock used or NOS rather than Omix-ada pieces-a lot of which are nothing short of crap.
The above post citing G503 will not do you much good. While the military parts will usually fit, the 2A/3A/3B parts will usually be more heavy duty and cost less. The classified on the 2A, 3A, 3B Pages, and Early CJ5 site would be my first picks for parts searching.
Whether or not you will need to go through the entire vehicle will be solely dependent on the PO's prior work and most often, there will be a bunch of PO's all with different ideas on what quality work means. If you see a bunch of cobbled up stuff, probably a good clue to steer clear. There are some real gems of cobbleism out there.
Some reason you are not looking at 3B's? I know some people don't like the high hood (personally, I don't mind it and found all that extra space to be VERY useful for modifications), but you do get 15 more hp in the F head and all the post mid 55's all got the 1 1/4" transfer case which are desirable improvements.
As for what can be fit under a 3B hood