Rough idle and smoke at idle after fuel filter change

[Echo]

I changed the fuel filters on my truck yesterday and also removed the cover on the water separator to clean out the drain area. I cycled the key 8 times to let it purge the air. It seemed to run fine yesterday with no smoke but today I started it and it is idling rough and I'm getting smoke out the exhaust. Also when I put it in drive the injectors are making more noise then normal. I did load a towing tune on it today before startup so I'm hoping reloading the tune will do the trick. Do you think there could be air in the system still?
Edit
I'm running the crappy canned sct tunes and my dpf is deleted

 

[Vinny07psd]

If you had air In The system still it wouldn't run

 

[Vinny07psd]

Did you seat the fuel filters correctly?

 

[Echo]

Yeah they both went in like they are supposed to. I did find a piece of black plastic and what looked like some very fine metal in the fuel bowl when I removed the old filter. I got the plastic bit out before I put the new filter in. I don't like where this is going, I just bought this truck 2 months ago.

Loaded a different tune, same thing still happening

 

[Vinny07psd]

Ya it sounds like you have an issue, yikes I don't know much about the 6.4

 

[Echo]

I drove the truck around being real easy on it and it seems to be back to normal now. Idles right and no more smoke. Beats me :shrug: my best guess is there may have been a little air in the system. I'm still learning about the 6.4 so if anybody has a theory I'm all ears.