Idles rough at stop lights just bought it only got 62 thousand miles what could it be

Do a compression test. Maybe that motor needs major repair.

check plugs, wires and mag pack its what your plug wires go to from spark plugs. Im thinking bad plugs or one wire is bad

engine rough at idle only?
is the check engine lamp on?
remove egr valve
start engine to blow out carbon
check egr to see if there is carbon holding the valve open
clean valve
reinstall retest

My Pontiac Grand Prix is also a 99, it has 216,+ thousand miles on it, it runs great, idles good, I need to replace the oxygen sensor tho as it shuts off on me while driving or sometimes coming to a stop. You might try checking the fuel filter and pump as well.

it might be time for a timing belt it often gets neglected. most need changed every 50 or 60 thousand miles

sounds like your lifters

Ahhhh!, if only we could turn back the hands of time. Is the vehicle sending any signals like blue smoke through the exhaust, or using a lot of oil. Possibly running on after the ignition is turned off.These are all indications of high milage wear internally. Rings, bearings, etc.etc. Low oil pressure? Blinking oil light when at intersections. Any of the above?

spray some carb cleaner on the passeger side of the intake manifold, right behind the alternator. it is very common for those to leak there and cause those exact problems

More maintenance history needed. Oil changed regularly, timing belt replaced at 60 K miles, Engine air filter & intake air hose inspection?
Causes of the problem you describe are many. Recommend you have a technician check your throttle position sensor for any bad spots in the potentiometer... most likely cause when there is NO Check Engine light.

The reason the check engine light is flashing instead of on steady is because it is missing bad and the car companies did this to tell you to stop the car as soon as possible to prevent damage. That is the only time the light will flash off and on instead of being on steady.
The cause is a little harder to diagnose. It could be a fouled spark plug, a bad plug wire, an injector, stopped up fuel filter. I can't remember if that car has the distributer or the coil packs but you could have a problem there. If you have never changed the spark plugs or fuel filter, it is well over a hundred thousand miles to do so now. They say to change them at one hundred thousand but 50 to 75 thousand is better and you will get better mileage. The fuel filter needs to be changed every 20 thousand miles now days because of all the cheap gas we have to put in the cars.
This is for mechanics or technicians. If no one out there believes me about the mileage on the fuel filter, then take the filter off and see what comes out the back. Looks like black water to me.