I never removed the door panel from a 99 Sport, but greasing the window tracks might not be a good idea. Have to qualify the term track, the part at the bottom of the window, where the regulator wheel rides or the rubber/felt where the window travels up and down. Check and see if the felt/rubber in the track (runner) has fallen out and/or twisted. Glue it back in there, with a good contact cement if it has. Clean the window runner, with a stiff brush, and lub with a dry lubricant, spray teflon or even graphit (don´t know what Jeep recommends).
Grease in cold weather, gets stiff, will stick and collects grit, sand and whatnot, makes thing worse in the long run, when used in certain places.
Save the grease for the window regulator, chain or cable. Though even there, chain oil, often works better than grease.
Sometimes the window runners, wear through, only solution is repalcement.
If the wheel for the regulator, that travels in the track at the bottom of the window, is making noise. You´ll often find, the shaft through the wheel is severly worn and grease doesn´t help much.