runs rough when cold
Grab a voltmeter and check the voltage on each battery individually. If one is really low, you might have a dead cell. If not, charge them fully then find a way to load test them. Wal Mart sells a low-cost Schumacher battery tester that will work fine. If either battery fails the load test, replace the pair of them.
http://www.walmart.com/ip/Schumacher...ingMethod=p13n
Are you getting a battery warning light at all? You'll need to make sure the alternator is charging, so once the truck is started and has run for at least two minutes, use a voltmeter to check the voltage across a battery. If it's not up into the 13V range, the alternator is going out, which is fairly common on the 6.0L. You have to wait at least two minutes after starting to let the glowplugs cycle off, if you test it too soon you'll almost certainly see less than 12V, which is common with stock alternators while the glowplugs are cycling.
Then you'll need to test the component that can actually cause the rough running issue. Use your voltmeter to test the FICM, while it's acting up if you can. If the FICM tests to less than 45V at any time, with the engine running or not running or while cranking, then that's what's causing the problem.
https://www.ford-trucks.com/forums/8...procedure.html
The FICM can be stressed by bad/weak batteries and a dying alternator, so you have to rule those two problems out first before you can really test the FICM as the root cause. If the FICM is bad, then call Ed at FICMrepair.com, and talk to him about his rebuild services. And depending on how the batteries and alternator tested, maybe a replacement alternator to help prevent the problem from recurring.
http://ficmrepair.com/
If you want, there are several tools you can buy that plug into the computer port on the truck and will check the alternator and FICM voltages without having to crawl around under the hood.
Stand alone units:
Edge Insight CS & CTS - Edge Insight Monitor with Color Screen & Color Touchscreen
For Apple products:
DashBoss | A Brain Scan for your Vehicle
For Android products:
Torque — OBD2 Performance and Diagnostics for your Vehicle








