Slow Idle?

I have a 00' XJ with around 175000 miles. My alternator died out the other day while I was driving and I ran off battery power to get off the highway and into the relative safety of a grocery store parking lot. I replaced the alternator, but now have a new problem that has left me scratching my head. Once the jeep warms up my engine starts to idle very slowly, starting off around 5-600 rpms and getting down to, well, as low as it can get before the engine will die-I hit the gas but it goes right back to the same place. Also-while driving after this occurs the acceleration feels off, almost like the engine isn't firing correctly. Once I get over 30 or 40 mph there doesn't seem to be a problem though. Any advice on the my issue may be or how to fix it?

if it makes you feel better my heep idles at like 300rpm most of the time. and it runs good to me, new: tps, iac, coil, plugs cap and rotor, air filter, mopar ccc, cleaned all grounds, tons of fuel injector cleaner, new k &n filter, and all new vacuum lines. i have no idea what my low idle is and i dont care cuz it never stumbles. my guess is the exhuast manifold gasket is bad.
i have tested all my sensors very often though. theres a possibilty my egr solenoid is bad though, everything else checks out fine

thx, but its running normal now. i read about the possibility of the ECS needing to reset after the vehicles battery is run too low, and i'm guessing that is what happened, because I changed nothing. I do love cars.