Howdy, first post be gentle

I just bought a 99 Cherokee about a month ago...unfortunately it sat for 3+ years (bought it off a buddy who has a company car)...so it does have a few issues, for instance its in the shop right now getting the corroded brake lines replaced...

But there is another issue...the Jeep will start up and idle just fine...it drives great...until I stop to, lets say, go to a grocery store...I'll run in and come out about 15-20 minutes later...I go to start it back up and it will idle really rough like its missing...I'll drive for 5 minutes or so untill it starts running smooth again...any ideas why this is so?

I've tried putting "dry" gas treatment in it in case it was water in the tank but no luck...the guy doing the brake lines said maybe plugs, distributor and wires (which he quoted me $250 bucks to replace)...I thought maybe it is a fuel filter issue since it sat so long...any suggestions would be appreciated...

 

A complete Tuneup would be first thing i'd do. Swap the fuel filter as well.

Is the fuel in it 3 years old?

 

yeah, several tanks of fresh gas has been run through it

 

I also recommend a tune up. Mine was running rough while sitting at idle when it was hot, I pulled they plugs and they were really worn down iridium platinums. I replaced the plugs, wires, cap n rotor and it runs super smooth now, and it was only a 20 minute job.

 

This should be your problem.. The 99-01 intake manifold is a poor design.. a couple heat sheilds on top of the intake manifold and a sleeve on injector# 3 solved my problem..

1803103 - 4.0L ROUGH ENGINE IDLE AFTER RESTART FOLLOWING A HOT SOAK
Date: 09/05/03 (supercedes 1802702 dated 09/06/02)
Model Year(s): 1999-2004

Description: NOTE: This bulletin applies to vehicles equipped with a 4.0L engine. This bulletin involves the installation of a fuel injector insulator sleeve.

Details: Customers may describe a 20 to 30 second rough idle following the restart of a heat soaked engine. This condition may be most noticeable when the engine is restarted following a prior 10 to 20 minute heat soak in hot ambient conditions of approximately 32 C (90ºF) or higher. This condition may be consistent with short city stop-and-go driving trips and can be aggravated by the use of fuel with a high ethanol content. Depending upon various conditions a MIL may occur due to DTC P0303 - Cylinder #3 Misfire.

This condition may be caused by heat from the exhaust manifold that following engine shut down migrates to the area around injector #3 and causes fuel vapor to form within the injector. This in turn may cause a momentary misfire of cylinder #3 until the fuel vapor is cleared of injector #3. The insulator sleeve lowers the injector #3 temperature to a point below which the fuel will not normally vaporize.

If vehicle exhibits a rough idle, and if a misfire of cylinder #3 is observed following a 10 to 20 minute hot soak, perform the Repair Procedure.

Parts required:
56028371AA Ignition Wire Shield

Repair procedure:
1. Cut insulator sleeve, p/n 56028371AA, to make two (2) insulator sleeves about 25-30 mm (1 in.) in length. See diagram.
2. Install one sleeve around injector #3, with the slit on the upward facing side of the injector. Install the other sleeve with the slit on the downward facing side of the injector.
3. Confirm sleeve is flush to intake manifold surface around injector.
4. Check injector #3 wire and ensure that the injector is rotated to a 2 o'clock position (from driver?s side of vehicle).