All sorts of weird stuff has been going on with my XJ recently and I figured I'd ask y'all for some help. A little background on it. I have a 2001 Limited 4.0 4x4 with upgraded 4 hole injectors, cone intake, magnaflow muffler and 2.5 in tailpipe, full sound system, and a heavy duty casting clearwater cylinder head. So now that I got that out of the way, here is the list of things that have been going on.

Passenger window only rolls down sometimes when I jiggle the button on my drivers door (rolls up fine every time though)
Rough idle, idles around 250 and flutters (lacks power when it does this)
I have quite the whistle when accelerating(I sound turbo'd)
The lights in the Jeep dim when I use my drivers switch panel for my windows
The little lights inside the switches on the door flicker randomly
Every once in a blue moon my gauge cluster spazzes and my oil gauge will go to 80 and then back to normal

I took the Jeep to have the codes run and got P1687, P0455, P0305. Which is a No bus code, large evap leak, and cylinder misfire.
I took it to Pepboys and they ran a full diagnostic on it and said they would love to tell me what was wrong but they "couldn't really test anything because my PCM is bad"

Just wanted to get some comments from y'all before I go spend a few hundred on a new PCM since I am a college student and funds are not as plentiful as I would hope LOL

 

I'd start with a thorough cleaning and tightening of the ground wires and battery cables. If you do a search there are several threads with locations and pictures. Take all the connections off, clean them and the contact surface up to shiny metal, maybe dab a bit of dielectric grease on there and put them on so they are nice and tight.

After that, you could try disconnecting the PCM, cleaning the contacts on both ends and reconnecting.
Most of the flickering/spaz'ing stuff is going to be a loose connection or bad ground.
The dimming lights when using the switch means high resistance in the switch or a tired window motor drawing too much amperage, or the voltage regulator in the PCM being flaky. If it's JUST the switch, I'd leave the PCM as the last suspect after exhausting everything else.

Please provide more info about the whistling sound - is it an engine sound? Exhaust? Body possibly? (I have aftermarket roof racks on my 95 currently - as it doesn't have the factory racks - and they "whistle" on the highway.)
This could be a leak in your intake area of some kind - meaning intake manifold, air filter housing, vacuum line - which would also cause poor engine idle. Whistling is not a common complaint so more specific info (a video with sound is often helpful) would help folks provide advice.

 

X2 on the grounds. I have this read time and time again when people post about anything electrical. A guy I know with a '99 Grand Cherokee was asking me if I had any ideas why one of his tail lights was not working. Thought I might know cause I own a Jeep. I told him every time something like this comes up on the forums that people say check your grounds. Sure enough.

 

O.P. I was thinking that you may want to check the wiring where it comes from the fender to the door. (I have no personal experience with this as the 3 Jeeps I've driven with any regularity have all been manual windows and doors - just how I like it!) A lot of folks have issues with the wiring fraying or pinching at the door and this would cause several of the symptoms that you've reported. You may want to open up the sleeve and check that the plastic sheathing on each wire is in good shape and repair it if it's not.

 

I will be home for Thanksgiving and have a place to work on the Jeep so I will go over all of the grounds and cleaning the contacts then since I will already be under the Jeep doing some brake maintenance. As for the whistle, my aftermarket intake is a fleabay special and I think that could be partially causing my problems so I am going to replace it with my old stock one or go pick up a better junkyard special intake and see how that goes. I will post back about how that goes sometime next week. The whistle is only when accelerating and it picks up around 2500 rpms to normally around 3500 and it is coming from around the intake or intake manifold area. I can hear air coming in somewhere around the right side of the engine by the intake manifold when the jeep is idling, but its just hard to narrow down exactly where it is coming from if I'm being completely honest.

 

I will go in and give those a quick look, but when I installed my door speakers and ran the wiring I repaired some of the wires that looked a little messed up in there and everything was still working fine after that, but it's worth a check. Ya never know with a Jeep

 

X3 on grounds and battery cables. BTDT

 

Grounds like others have said. I would also check your battery cables, connections ...battery ...and *especially* the alternator's output and belt tightness. I've experienced a similar set of problems (a land rover though) only to find out after much time and energy (and money) was spent, that it was the alternator belt wasn't tight enough. What would happen is at idle and residential road speeds, especially with lights, blower motor and ac off, the belt would grip enough and the alternator would charge fined. The gauge cluster would act normal, no problems whatsoever. After a period of higher speed driving, especially with lights on ..and more load on the alternator, the belt would slip (some, not completely), and things would start flaking out as you described. I'd get home and start checking things out and couldn't find any problems (again, at idle speeds).

Ultimately an alternator shop I took the alternator to noticed the worn pulley grooves and explained the issue and he was right. I had to replace the alternator pulley as it had worn enough that it no long would fit right into belt grooves (the ridges were 'sharp') and of course the fairly new belt had become 'glazed'. On Land Rover V8's it's fairly common to mis-route the belt. The way most people **think** it should go as logic would seem, is the wrong way ..and the wrong way, although seemingly tight, doesn't have quiiiiite enough tension. But I've seen the same set of problems affect other makes of vehicles too.

So check the charging system starting at the integritiy of the belt and alt pulley. It may not be your problem, but they are easy things to check and rule out.