It sounds like you have an Edelbrock "Performer" aluminum 4 barrel intake manifold, which is a good choice for a 304.
A 500 cfm 4 barrel carb would be a better choice for a otherwise bone stock 304. With a mild cam and a free flow exhaust, the 600 would work.

The stock Motorcraft 2 barrel would fit with an adapter, it works better off-road than the 500 cfm Holley 2 barrel. A Motorcraft 2 barrel 2150 from a late model 360 Grand Wagoneer has an "Aneroid" on it for altitude compensation, if you wheel in the mountains it might be a good choice, it bolts on exactly like the stock 2100.

Fenderwell headers usually place the mufflers right under the floorboards on the sides of the CJ, with the tailpipes turned out ahead of the rear wheels. I used to have a CJ setup like this. They are noisy when driving next to the center divider on the freeway, I eventually rerouted the tailpipes to the rear.

As mentioned, a large diameter (3") single exhaust works better and sounds better, too. They make headers for CJ 304's that tuck unto the framerails and allow for a conventional exhaust routing. I usually ran 2-1/4 (304)or 2-1/2" (360 & 401) headpipes to the inlet of a single 3" inlet cat-converter, then 3" pipe to a single Magnaflow muffler, then out the left rear corner of the Jeep in the same location as the stock system. I usually was able to reuse the stock exhaust hangers and onderfloor heat shields, too. The single exhaust has a more even tone, not raspy like the two turbo mufflers under the floor.

The stock CJ AMC 304 iron exhaust manifolds actually flow very well, not much to be gained with headers, especially if the engine is basically stock. The stock manifolds seal better to the heads, too. I like to use factory Mopar exhaust gaskets, spec them out for a 1989 SJ Grand Wagoneer, much better than any aftermarket header gasket! (I hope they are still available!)

Hope this helps!