Do you have stock size tires? If larger than stock, regearing the axles to lower gears will be the number one improvement to off-line driveability.
If you're YJ is a '91+, I'd recommend a 62mm throttle body (like the ones I sell). They greatly increase airflow to the engine and it removes the taper beneath the throttle plate that restricts airflow for the first 1/4" of throttle movement. Throttle response is increased dramatically.