Right side door locks and windows don't work anymore

[LizardRunner]

Having just been released to drive by the doctor, after my femoral artery by-pass surgery. I finally got to get back in the red lizard and, dead battery caused by a bad alternator. I replaced the alternator and now the right side and rear hatch seem to be dead. No windows (actuated from either side and no locking, either with the switch or the key fob. I just need ideas of where to start checking, cause I haven't a clue what would cause this. Thanks for any help folks.

[NW99XJ]

Well, let me first say speedy recovery Chip, hope things heal up well and good.
Now on to the good stuff..... Lets start with the obvious....check fuses.... take a look in the interior fuse panel as well as the one under the hood. That seems a tad bit redundant and elementary I know, but its a good place to start.
Now going off of your statement of only the DS and Rear hatch are the devices not working, i'm going to assume that the Passenger side is still working fine.
To me this may narrow things down to one of two most probable causes;
1.) either a bad switch, or....
2.) broken/corroded wire.

Neither one is going to be fun to deal with, but will be easy enough to diagnose.
This is going to involve some interior removal, namely the door panel and kick panel.
Once the door panel is removed - or at least loosened up from the door itself - you'll want to use a Multi-Meter or a test light and start probing the wires at the back of the switches. You'll be looking for voltage going in and coming out of the window switch for the corresponding sides.
I have found a rough wiring diagram that MAY help you......
http://1.bp.blogspot.com/-gl9VYswMIWU/T0Gc1sonFfI/AAAAAAAAARw/2wvocsClex4/s1600/jeeppdm.jpg

HOWEVER........
The 2004 WJ's uses door modules in each door that communicate through a data buss called PCI ( Programmable Controller Interface) buss.
It is basically a peer to peer network meaning that any module on the network has the ability to communicate on it's own. Both the DDM ( Drivers door Module) and PDM ( Passenger Door Module) share a common power and ground feed as well.

The BEST way to diagnose this would of course be to use a DRB3 Scan tool, and do a module scan search to determine if both modules are communicating to the PCI.
This would tell you whether or not the modules are working or have failed due to an internal issue, or a wiring failure.

Since most of us dont have this tool, we have to do things the old fashioned way, and thats through a lot of probing with the multi-meter or test light.

I would also spend some time doing a very thorough visual inspection of the harness (and of course ALL of its wires) that go from the door to the kick panel/ A-pillar.
I have heard there is a common issue with broken wires in the boot, that can cause these symptoms.
Fixing a broken wire is easy, either use a good solid crimp connection or solder the two halves back together and use shrink tube to seal & protect the connection.

This is most likely going to be a lengthy process, and once started should not be stopped to maintain progress, and follow through. I would recommend doing this in a garage, as there is a good chance the door is going to be open for quite a while. Because of this, I would also recommend starting the engine once every hour or two, to maintain battery voltage.

I hope some of this helps, good luck!

[LizardRunner]

Thanks Josh, I have the factory shop maual for wiring diagrams. I can rent/borrow the DRB3 scanner locally (have a buddy that will do that from his work). When I find out what went wrong, I'll post the fix here.

[LizardRunner]

Okie Dokey now, Last evening I got time to work on the red lizard to find and repair this issue. Checked every fuse in the both blocks, all were good, tested all the relays, same results all good. Checked the wiring harnesses from body to doors and no broken wires, did find that the black ground wire in the drivers door had been spliced back to gether previously. I then struggled for abot 10 minutes trying to get those boots back on but with out a homemade tool, it isn't happening for now. So, after all that I was ready to toss it in for the night but had to make a run to the store. Now this is where I became convinced that my vehicles simply do stuff like this to get my undivided attention, because I decided to try the passenger windows that had stopped working and they worked. I got to the store and tried the door locks, they worked. I tried using the fob lock and it worked. Every thing that had gone south is now working just fine, like they should and as far as I can determine all I did was show the RL that I do love her and will fix her as soon as possible when things go bad.

Side note, this same sort of thing happened with the Green Lizard (who I've seen lately and the N O has really fixed her up nice, taller lift, new paint, etc.) which would periodically give me fits until I showed it I did really care about it working right.

[NW99XJ]

Well that just figures..... HA!!!

[OrangeXJ]

Okie Dokey now, Last evening I got time to work on the red lizard to find and repair this issue. Checked every fuse in the both blocks, all were good, tested all the relays, same results all good. Checked the wiring harnesses from body to doors and no broken wires, did find that the black ground wire in the drivers door had been spliced back to gether previously. I then struggled for abot 10 minutes trying to get those boots back on but with out a homemade tool, it isn't happening for now. So, after all that I was ready to toss it in for the night but had to make a run to the store. Now this is where I became convinced that my vehicles simply do stuff like this to get my undivided attention, because I decided to try the passenger windows that had stopped working and they worked. I got to the store and tried the door locks, they worked. I tried using the fob lock and it worked. Every thing that had gone south is now working just fine, like they should and as far as I can determine all I did was show the RL that I do love her and will fix her as soon as possible when things go bad.

Side note, this same sort of thing happened with the Green Lizard (who I've seen lately and the N O has really fixed her up nice, taller lift, new paint, etc.) which would periodically give me fits until I showed it I did really care about it working right.

I hate elictrial problems one day the buggy went dead. Nothing no ign,fuel valve lights. Pulled the panel to get to all the switches and OMG it was a bird nest of wires. Now the fun part they were all red making it almost imposable to trace them. Found nothing obvious called it a day. Next day Iwent to work on it again walked up to it and heard a noise the fan was running (opps left the switch on) turned on the ing/fuel valve hit the start button and it fired right up. Don't know caused it and have had no problems with it.

[NW99XJ]

I hate electrical gremlins...... such a pain.
Nothing worse than trying to troubleshoot an INTERMITTENT electrical problem.

[LizardRunner]

An adendum to this issue. It happened again and this time... The black wire was busted clean. I've repaired it with a butt splice and all is good and proper again. Upon inspecting the newly discovered busted ground wire, it did not appear to have been seperating prior to the complete break but who knows. It is after all "A Jeep Thing" :smiley-laughing021: