I don't think you can really do anything to alter either of them. The throttle is a cable throttle and immediately starts tugging on the throttle body as soon as you move the pedal. The engine is torquey down low and makes a lot of noise which adds to the sensitive feel. The clutch is non adjustable and is hydraulic, nothing you can really do there either.
The clutch is a "long" pedal travel, but it's not all that long of a clutch to engage. It doesn't engage immediately off the floor and it's done engaging before the pedal is fully let go. I think if you give it some more time you'll get used to it and not care so much. You will get better at learning the useful range of the clutch and will drive it accordingly at that point. Every manual vehicle is different. Yours sounds perfectly normal for a TJ.
You can try adding a spring or two to the throttle but when I did that, it just made the throttle feel weird to me, It added some resistance but also made the gas pedal harder for me to use, so I took them back off. You'll get used to it too, you just learn to make minor adjustments to the gas pedal rather than burying your foot in it much, at least when starting from a stop or at low speeds.