I've traced the fuel lines and have found them to be intact. Im beginning to suspect glow plugs. I recently replaced the GP controller and the engine started perfectly for a month, then the hard starts began. After cranking for several seconds, the engine fires up and a big puff of grey smoke blows out of the tail pipes, smelling like raw fuel. If it is the GP's it would explain why the engine fires right back up after I've been driving for a while.

Also checked the relay for a jumper and didn't find one. Everything looks factory.

Could it be that the new GP controller burned out one or more of the glow plugs?

Glow plugs can burn out especially factory plugs.

While I do think it's always a good idea to check your glow plugs every year I don't think it's your whole problem. I've have trucks start better than you describe on only 4 glow plugs.

You stated that the fuel pump runs for a few seconds after key is shut off. The 1/2 ton is set up to run for 5 seconds after shutdown and the 3/4 and 1 ton 6.2s are set up to run for 30 seconds after shutdown from the factory. I have several of these 6.2 trucks and have found that the Gpc's currently available don't last very long. At 100 bucks apiece can get expensive fast! My trucks are rigged up with a solenoid and push button on the dash to replace the Gpc. I hold the button down for 5 to 10 seconds depending on outside temp and they start right up. Your Gpc is probably burned out. Good Luck!