Ford F350 shakes after shifting to overdrive

I have a 04 F350 FX4 Crew with a 6l diesel and about 52,000 mi. I lost power the other day and was only able to maintain 40 mph on the highway. I changed the two fuel filters and have the power back but now the truck shakes when it shifts into overdrive.
And it could be my imagination but it seems the engine is idling rougher than before.