I have a 99 2500 4x4. I just performed the W-T ground mod and now i have a flashing WTS light. Truck has brand new batteries, 2/0 battery cables from CE auto electric. Just don't know where to go. Any help is much appreciated. 

If the problem statrted after the mod I would go back and check what you did to be sure all is as it should be. Did you disconnect the batteries while doing the mod?

Yes the batteries were disconected. I was going to do an APPS relearn because the aux battery crapped out. This whole truck has been a nightmare. I've had it 4 months and have only been able to actually drive it 1 time. 

I never had this much trouble with the common rail used to have

What other issues are you having? I kind of figured all was fine until you did the ground mod.

Looks like maybe ECM ground is a good place to start.

https://mopar1973man.com/topic/7855-flashing-wait-to-start-light/?page=2

 

Are there any codes set?

All of it did start after the mod. I got the truck with a exploded t case. 

I'll recheck all my grounds. Thank you

You say one battery went bad. I'd say it's fairly uncommon for one to go out and not affect the other. Was it just that battery's time, or did something abnormal cause it to go bad? If the alternator cooked it, why? Are the cables in great shape? Some guys report good cables, then find the cable is corroded under the insulation.

2 hours ago, Chase Johnson said:

This whole truck has been a nightmare.

Sounds like maybe the transfer case was a nightmare if it took four months to get it replaced, not sure how that and an electrical issue makes the "whole truck...a nightmare".

Alternator is good. AC noise is only about .01. I replaced both batteries. All battery cables are brand new. I bought a 2/0 kit from CE auto electric. I've been able to start the truck and move it around everytime with no trouble. This weekend I'll recheck grounds and wiring. Where I'm at it gets dark just after 5 and i work until 6.

Double check the ground wires make sure you got them all hooked up. Just make sure the ECM and VP44 are getting good ground. 

 

Flashing Wait To Start is typically a ECM error of some sort. You might grab a code reader and see what codes are displayed. 

I'll recheck them this weekend. Thank you for all the replies. Much appreciated.