Powerstroke Pulsing during slow acceleration?

[metalmulishamunky]

Hi Everybody! I just bought a 04 F350 with the 6.0 and 114,000mi. I took it hunting and had to make a river crossing (didn't look to deep) needless to say i hit a deep spot and had water come over the hood, it sucked water and the truck died. I got it started and it struggled for a little while but it finally stopped white smoking and we got the filter dry. The truck was running normal (as normal as I could tell only owning it since last tuesday) I drove it to a friends house later that night with a round trip of about 60-70 miles and it ran flawlessly. Today when I drove it, it ran fairly normal, had plenty of power but when if I accelerate slow-normal the truck surges as it accelerates . It doesn't happen while holding speed or while accelerating quickly. The truck never threw any engine lights and didn't throw a water in the fuel light. Do I just need to bear with it for a little bit? it also has a random rough spot in the idle but it doesn't happen too frequent. I've swamped my 360 gas im my dodge 1/2 ton before and it took about a week for the truck to start running 100% normal again.
Can anyone help me out please?
I've done my share of work on gas motors but this is my first diesel and I'm pretty much clueless, I know the basic mechanics but that's about it. Also I've heard that there is a water separator in the fuel filter with a drain at the the bottom of it but i have no Idea where it is.

Please Help!
Thanks!!

BTW Truck is stock with the exception of a PTO control computer that was in it when I bought it but I haven't touched it

[no-tel-in]

so you just started it right back up after taking in water???

[metalmulishamunky]

it took a little bit to get it started, we tried it a couple times then let it sit about 30-45 min then tried it again and it fired right up but didn't have any power, we pulled the filter cause it was soaked and the truck ran crappy for about another 20 min, then it seemed to run normal, we drove it about 10 miles with the filter out the window to dry it and re-installed it when it was dry and the truck started running normal, and ran normal all night. today is when i noticed the surging during slow accel. Could I have a dirty EGR?

[no-tel-in]

Do you have AE or other scan tool?

Change all the fluids, oil/filter, fuel filters, air filter, and probably differentials if you are concerned anout the gaskets on the covers

[metalmulishamunky]

no I don't have a scan tool
I don't think anything got contaminated
Ford says a chunk of carbon might have broken loose and got stuck in the EGR, other than that they just recommended changing the air filter and running it a little bit just to make sure

[forddieseldoctor]

did you remove and drain your charge air cooler? They have been known to hold water after it gets sucked in.

[metalmulishamunky]

i thought we got to pretty dry but I guess not, I pulled it today after work and drove it about 2mi and the surging was gone, i put it back in and it started again but not as bad.

I'm gonna replace it and hopefully it will fix it.