Rough running Ls model 4 cylinder, 2000. Engine idles in N and Park and throttles fine. In any gear it hesitates runs rough and bogs. Check engine light is on also. Oil,plugs,filter,wires and fuel filter all ok. Any ideas? Thankyou in advance for any help.

This sounds like you might have a bad plug wire or something else in the ignition system is arcing to ground. A quick way to verify this is to run the truck in Park at idle. Next, spray the ignition wires with Windex. You'll notice the truck starting to rough up and might even see the bad wire arcing to ground. A complete tuneup would be recommended in this case.
I hope this helps! :)

Sorry guys i was late with my feedback... So here it goes.. I have no check engine light.... Currently running the stock tune as well.. The car has no tps, pcv or egr valve.. It is all controlled by the electronic throttle body which i recently cleaned but didnt help with my problem. I ordered a new fuel pump as well, just didnt get the chance to install it yet. Cant change the fuel filter as it is builtin within the pump. However, shouldnt the fuel pump or fuel filter cause engine stalling, bucking and hesitation? I doubted the fuel pump could be causing this since the problem only occurs at idle. By the way, there is no missing on any of the cylinders.

Here's a link to your misfire. P0301 Dodge Cylinder Misfire Fault Detected ,check this video out. Why Do Engines Misfire P0301 Code

use a couple of quality injector cleaner in the tank
run fault codes
remove and clean injectors
check fuel pressure

Hello I have a 1995 Sonoma 4.3 with 150.000 on her and she ran great tell last week went to pick up a lite trailer and dove it home no problem drove it all day after that. The parked it running fine and next morning it won't hold a idle but clears up at 3000 RPM runs fine drop in gear and it won't stay running??? Cleaned TBI and there was a new fuel pump and filter put on it less them 7.000 miles ago. Found vacuum leak on the booster to manifold fix that still runs like it is misfiring??? Any help would be great thanks no check engine light on.

Do you know what engine scan data is ? Disconnecting sensors is not the way to find a problem ! What is the computer seeing as data input signals . Is the vehicle in closed loop fuel control , is the EGR opening when it shouldn't be , Is the PCM controlling the idle air control valve or is the vehicle drive by wire (electronic throttle control ?
005 Idle Speed Problems Idle Air Control Test
007 Idle Speed Problems Scan Data for Idle

A faulty throttle position sensor or an intake air leak near the mass air flow sensor.

Most likely your throttle position sensor is faulty. You could have a vacuum leak as well. Most probable cause is a bad sensor. Is your check engine light on? Have you checked your engine codes? You can go to autozone.com and register for full free online repair manual.

When you have the car in gear there is a load on the engine. If you are for some reason not getting good fuel then its trying to compensate by kicking the idle up. When you are just in park there is no load so its not struggling. Regularly using a fuel system cleaner will help with rough idle, as well as hesitation. Also it might be good to check the fuel pressure regulator.

Check the air filter hose. My '99 Protege was idling rough and would sometimes shut off. The air filter hose was cracked half way around. I replaced it (easy just loosen two hose clamps and pull out the sensor) and the car is running fine.