Service Engine Soon, Water in Fuel, Overdrive, Cruise, Wait to Start all flashing when I put the key to on. Whn I start they continue to flash, then they stay lit constantly, then the truck runs rough and finally stalls.

Can't reset the DTCs. Tried to reprogram to stock but programmer said batteries too low. Pulled both batteries took them to checker and they recharged batteries and they checked good. Put them back in the truck and all lights gone for about 10 seconds then they came back again, truck running rough them it stalled. Went to start it and the batteries acted like they were low and it wouldn't start. Pulled the batteries again and took them to autozone this time, they said batteries were low and needed to charge at least an hour. They charged them and they check good. Cleaned all terminals and put batteries back in truck No lights for at least 5 mins, then same thing, warning lights flickered then stayed on hard and truck stalled. I also hear relays clicking in the dash and under the hood. Even with the key off.

DTCs are
P1690
P0755
P0743
P1754
P0381
P0230
P1662
P0603
P0470
P1139
P0750
P0755
P0743
P0541
P0640
P1105
P1106
Any help would be appreciated. Also while truck running put a voltmeter on the batteries, both were 12.30 volts. Also has a noise like a relay latch or faint turn signal under left Battery. Sound is heard every four seconds.

I took the Alternator and got it tested. It tested bad, I put a brand new one in, same problem.

 

P0755 Shift Solenoid B Error
P0743 Torque Converter Clutch Sys Electrical Failure
P0750 Shift Solenoid A Error
P0640 Manf Intake Air Heater Control Circuit
P0541 Manf Intake Air Heater Circuit Low
P0470 Exhaust Back Pressure Sensor Circuit Error
P0381 Glow Plug Indicator Circuit Error
P0230 Fuel Pump Relay Dvr Fail
P1139 Water in Fuel Indicator Circuit Error
P1105 Dual Alternator Upper Fault (Monitor)
P1106 Dual Alternator Lower Fault (Control)
P1662 EDU_EN Output Circuit
P1690 Wastegate Control Valve Error
P1754 Coast Clutch Solenoid Circuit Error

P0603 is a KAM Error... assuming your running a chip. P1105 and 1106 are showing an alternator fault... does you truck have dual alternators. A bad alternator can have some weird affects on these trucks. Atleast get these codes up for the gurus to come thru and clean up.

 

It doesn't sound like your batteries are getting much of a charge at those places.

Invest in a good battery charger that auto-transitions from charge to "trickle", and let them charge for about three days each. You don't want a real high charge rate, as it creates excess heat and hydrogen gas. The excessive gas tends to displace too much electrolyte, causing it to "boil over". Not good. A slower charge will be much healthier for each battery.

Properly done, a good battery charge takes some time.

Buy a quality electrolyte hydrometer to verify the charge state. A good one will include a thermometer for compensation.

Pop

 

Good advice Pop, reps sent.

 

And in addition to SpringerPops excellent advice, make sure that every connection is clean and corrosion free.
A bad connection is just as bad as a dead battery: no power gets through.
I can't tell you how many times I've gotten dead cars started right off of the tow truck simply by cleaning the battery posts.

 

I think Pop and Dan got you on the right track. Your batteries are weak. My alternator just died this last weekend but I was able to see it coming - I have a voltmeter in my gauge pod and it was reading 12v while driving. I was able to charge the batteries overnight with a trickle charger and swap out the alt the next day. The truck started right up. I let it idle for 15-20 minutes with the high idle on my DP and immediately the volts shot up to 14v. I started the truck for the last two days and let it run and no issues. Either get those batteries charged or replacements are need. BTW, you need to replace both batteries. good luck.