Need Help with Tranny

Hey guys I have looked at this website for a while but really haven't had any issues so I haven't ever posted, but just today I was towing about 7,000 lbs. Everything was great while towing. As soon as I had unloaded the boat I noticed when I was driving later in the day every time I slowed down at about 15MPH I would feel a the tranny make a clunk. Any ideas what this is? Just to let everyone know two weeks ago I lifted my truck but I have shimmed the carrier barring and dropped the driveshaft so there is zero fibration in the drivetrain. I think that I might have a tranny issue but just not sure what. Also no recalls have been done to this truck.

My second issue has been sometimes I will go to take off and the engine will gain RPMs and it will go really quiet and not make any power and then I will see smoke coming out of the exhaust. If I let off and stop and try again usually it is gone. I thought a few months ago I had an EGR issue with the cycling loud to quiet idle issue but they re-flashed my truck and it was gone. I think that this might be an EBP sensor issue.

Sorry for the long post but I appriciate any input that you guys can give me. My truck is going to the dealer on Tuesday.

Ford 2004 Ford F-250 4X4 Lariat CC SRW
6.0 Diesel
Magnaflow 4" Exhaust
Auto Meter Guages