You did not check your FICM properly.
First and foremost, if your batteries are older than 30 days old, remove them from the truck and have them individually load tested. If they are marginal or fail replace.
Ensure the batteries are fully charged.
Do not bother testing the FICM until the batteries are checked and fully charged. It will not give you proper readings.
Then follow this little snippit from Swamps Diesel:
How to check my FICM voltage with a multimeter or voltmeter
***FICM voltage tests should be performed with the engine oil COLD (ie, close to ambient air temperature). This will force the FICM into it's inductive heating strategy, which will give you a worse case scenario/voltage reading. If the engine has been run (within 5-6 hours of this test), then the warm engine oil may not give you an accurate FICM voltage.
On all 2003-2007 Ford 6.0L Power Stroke diesel engines you will find the FICM bolted to the drivers side valve cover...you may need to unbolt the coolant reservoir from the 'cowl' so that you can get your arms/hands back there to work on the FICM.
You don't need to drain the coolant...just unbolt the bracket that hold the coolant reservoir, and gently move it as far out of your way as possible. Be careful, as there is a plastic coolant connector that can be cracked if the coolant jug is handled forcefully.
On the top of the FICM, you will see a diamond/oval shaped metal plate...remove the two screws from that plate (Torx#20).
under that plate you will either see 7 "lugs"...or 4 "lugs" (depending on the year of the truck)...
if you have a "7 lug FICM"...you want to put one lead from your multimeter onto the upper left "lug"...and the other multimeter probe to ground (bare spot on the cylinder head, alternator bracket, negative battery terminal, etc).
If you have a "4 lug FICM"...you will want to check the lug on the right (closest to the drivers side fender).
be careful NOT to lean the probe on the FICM lug...over onto the aluminum case...you might let the smoke out, LOL...
Have someone turn the key to the 'on' position (don't crank it yet)...and see what your FICM voltage is. It should be >46volts.
Next have someone crank the engine...and see what the FICM voltage is while cranking...again..should be >46volts.
Go ahead and start the engine...and see what the voltage is while idling.
If the FICM voltage drops below 46 volts...then it is "bad"...
we have seen FICM's as low as 17volts...some 19v's...some in the twenty's and low thirties...
obviously...the lower the voltage...the 'worse' the FICM is...and the more likely that (cold) rough running would be a result of a bad FICM.
however..if you email (or call) us and say that your FICM is dropping to 43-44volts...while low..I think that you may have some underlying injector issues that may be contributing to your cold rough running, as much as the slightly low voltage FICM
You can email any questions to firstname.lastname@example.org
; however, if your voltage IS low...then your FICM is bad, and you can place an order at the following link. Swamp's Webstore - Custom Electronics
due to the high demand of our (48v &/or 58v) Heavy Duty FICM's, we are typically running 2 days behind on current orders...if you need express delivery, please make a note in the comments section during your online checkout, and we will call you with shipping options and rate quotes.