My 87 jeep wrangler shifts fine when not running. will not manually shift into gear when running?

Sounds like your clutch is not disengaging. when you press on the clutch pedal you should feel the resistance of the clutch pressure plate. There is a pilot bearing in the flywheel when it goes bad it continues to turn the transmission mainshaft not allowing your gears to line up for a shift, but you have noticed a bad noise if this were the cause. Or your clutch hydraulics have gone out. check your fluid level. if low you may have sucked some air into your system. you will have to bleed the lines as you would for car brakes. The other possibilities are bad clutch master cylinder or slave cylinder,