Most likely the fuel pump in the fuel tank. This summer mine would do the same after driving it a lot. I thought it might be trying to vapor lock and making the fuel pump work all the time and harder, but I never really had any performance problems.
I haven't noticed it lately, but I've put the top back on for the winter so I don't hear as many noises now (like the engine when it knocks and ticks).
I'm not a lot of help, but at least that should give you a starting point.
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92 Canyon Blue Wrangler YJ 4.0L - with some fun goodies