I would start by cleaning your Idle Air Controller (IAC):
https://wranglertjforum.com/threads/how-to-clean-your-iac-idle-air-controller-valve.662/
If that doesn't fix the problem, consider replacing your Throttle Position Sensor (TPS). Sensors in our TJs should always be replaced with the Mopar version, as aftermarket brands are typically junk. I had a similar issue where the RPMs would jump to about 2,000 when I would push in the clutch. A new Mopar TPS fixed my issue.