Diesel Bombers - 94' Chevy 6.5td running rough

Hi, I'm fairly new to the diesel world and I'm running into a slight problem. My fuel line recently busted and I replaced the line and bled the lines up to the gp's and now my truck is running extremely rough and has trouble starting. I need to use ether to get it started in the morning or if I let it sit for more than a couple hours. Basically, if the truck is warm it'll start right up. When I do finally get it started, it runs extremely rough and ticks. Also, its blowing darker smoke when I put down the pedal and a bluish/grayish smoke at an idle. Please help!