The engine's I'm not sure, but they are V8s so still have some value. Depends on the condition of the engine, I usually see complete running 304s/360s run from $250-$600. If they are rebuild cores as you said, $100-$250 maybe?
Transmissions all depend on the model. 3 speeds are not much value unless someone is replacing a broken unit. $free-$50
4 speeds are either valueable (T98, T18 truck type, sometimes a T176) or can't give away (SR4, T4).
I would guess headers are $50-$150 depending on condition.
I know there are still people out there using AMC parts, but I have bad luck on this board selling CJ parts. I think a lot of the CJ / AMC guys are more old school and not online so much.