'01 Cherokee Transmission Problem

When the jeep is off, there is no problem shifting gears (manual transmission). However, when jeep is running gears wont shift without being jammed; the only way to get it to shift is to shift the drive from 2WD to Neutral, then gears shift fine. Is it a clutch problem?

The trouble may be due to too much difference in tire sizes.

This is most likely a clutch release problem i.e. the clutch is not being fully disengaged. Is the pickup point of the clutch engagement close to the floor? If so that also points toward the release system. I believe this jeep has a hydraulic system so check the fluid level in the master cylinder reservoir. If the pedal feels spongy, you might try bleeding the system. If the level is okey and bleeding does not improve things, you probably need to replace the clutch master cylinder and/or the clutch slave cylinder.

Hope this helps.