engine runs rough after driving awhile

[Boatwheels]

my truck is a 07 6.7 3500 chassis cab manual six speed. The problem happens after driving for more than a half hour. The engine runs rough all rpms. loses power like I dropped a cylinder. the emissions have been deleted. the truck has a h&s xrt tuner tuner was installed at 100,000 miles truck is at 240,000 now. sitting at a light when I take off blue smoke. problem comes and goes. replaced fuel and air filters. runs fine at the start of the day. no lights on dash. truck never had a problem all original.