Replaced ctm unit and truck won`t stay running.

This site does not do well on abbreviations like 'Ctm'. Please always include full explanation. 'Central Timer Module (CTM)'.

https://www.google.com/search?q=1999+Dodge+Durango.+CTM+wiring+diagram

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ctm = control timer module
go www.dodgedakota.net --and there are forums there that may be of help to you
the problem may not be the ctm but in the pc data bus network to which it is connected ( wiring , fuses and bad connections )
in other makes of vehicles is is known as a body control module (BCM) and does the same functions as what they do

It's called the Central Timer Module (CTM) and it's either on the left side next to the driver's feet behind the trim panel, or behind the glove box on the right side. They changed the location sometime between 2001 and 2003.

I have a manual for a 2004 Dakota that is probably similar to the 2006 electrically. Dodge never called it a Body Control Module; earlier models did have the Central Timer Module (CTM) which functioned like Body Control Modules in other manufacturers vehicles.
In 2004, the CTM was replaced by the Integrated Power Module (IPM), which consists of the Front Control Module and Power Distribution Center, and is located next to the battery on the left inner fenderwell (the Front Control Module is underneath the Power Distribution Center, where you will find relays and fuses). There are several other modules which control various functions, and they communicate with each other through the Programmable Communication Interface (PCI) bus circuit, also called J1850.
The Front Control Module controls all exterior lights, except brake lights and turn signals, and the windshield wiper functions. Other modules (PCM, TCM, antilock brakes, heated seats, instrument cluster, power locks/power windows/power mirrors, etc) control other functions, but all communicate through the PCI bus.

The most likely cause of this is a failing Central Timer Module (CTM). The CTM directly supplies power to the headlamps and dash illumination. The head lamp switch sends a signal to the CTM, and then the CTM sends power to the lamps. Replacing the CTM should take care of this.

The Central Timer Module (CTM, called BCM on some vehicles) supports or controls:
Automatic door lock/central locking
Battery protection
Chimes
Exterior lights (park lamps, fog lamps, headlamps)
Interior lights
Intermittent wiper control
Power lock control
Remote keyless entry (RKE)
Vehicle Theft Security System (VTSS)
Remote radio control (from steering wheel)

It covers all the problems you described except the 4WD controls. I suspect you may want to have the CTM checked, or do like I did and just replace it (used about $75-$100 on eBay). Make sure you get the part number on yours and match the number portion (not necessarily the two letter suffix) EXACTLY.
It should be located behind the kick panel to the left of the driver's feet (that's where it is on my 2003 Dakota), but may be to the right of the glove box (have to remove the glove box to get to it).

Check these fuses again:
In the Power Distribution Center (in the engine compartment, left fender panel) Fuse #3 (20 Amp) Fuse #7 (40 Amp), Fuse #12 (20 Amp) and in the Junction Block (on the left end of the dash) Fuse #1 (15 Amp)
Use a test lamp and make sure that these fuses have power. All of these fuses should all have power at all times, regardless of ignition switch position. If they are all good and have power, then you probably need to replace your Central Timer Module. All of the circuits you listed are dependant on this module for operation.

The Central Timer Module is located at the left kick panel.

Central Timer Module System

The CTM is available in a BASE or a HIGHLINE configuration. The BASE and HIGHLINE CTM provide the following features:
• Battery saver functions for exterior and interior lights
• Cargo lamps chime warning
• Courtesy lamps
• Dome lamps
• Dome lamp defeat
• Door ajar switch state
• Fog lamps
• Headlamp time delay
• Intermittent wiper controls
• Low and high beam head lamps
• Optical horn
• Park lamps

In addition, the HIGHLINE CTM provides the following features:

• Central locking
• Door lock inhibit
• Driver door unlock
• Enhanced accident response
• Horn chirp
• Optical chirp
• Power door locks
• Remote keyless entry (VTSS)
• Remote radio

check for battery short inside battery have some one check for ac voltage in battery and alternator out put,,,headlight switch would be next to check or replace

Check for moisture under the interior carpeting.
I have see it cause this when the wiring gets wet on the connections from the door switches. Other wise you are going to have to get a meter and check all the wiring to each door and the lamp switch.

It's possible it's the headlight switch, but I would suspect the central timing module (CTM), Chrysler's version of the BCM for 2003. It's located behind the kick panel to the left of the driver's feet, and is held in by three screws. Replacements (used/rebuilt but most warranteed) are available on eBay at
https://www.ebay.com/sch/i.html?_from=R40&_trksid=p2380057.m570.l1313.TR0.TRC0.H0.X2003+dakota+ctm.TRS0&_nkw=2003+dakota+ctm&_sacat=6000

Get the part number from yours, and ensure you get the same part NUMBER, suffix letters may vary (especially the last letter). Make sure you are NOT getting a BASE version (marked on the part number label) if you have power door locks, etc.