6.9 idi missing, puffs of white smoke

Hello all. Well first off this is my first diesel and I'm a decent mechanic but nothing like what I've read on a lot of these forums. Here my problem. I recently replaced the fuel selector valve and due to being low on funds couldn't afford enough hose to completly replace from tank to selector valve but did install filters as recommended for warranty purposes. Everything ran fine I spliced the lines from Teflon hose to rubber with the correct fitting ran great for weeks. Then all of a sudden I am getting a miss and what sounds like a compression knock at all rpms. It's not consistent though at times it will idle like nothings wrong others it makes a loud puffing noise from the engine and a ploom of white smoke comes out. I noticed that because the fuel filters were glass that I was getting a lot of air bubbles from both tanks so I chocked it up to the filters leaking or connections and totally removed them. Still the same problem reading through forums here I have done the cracking lines with no real noticeable change although I do know that my return cap on one cylinder does leak a little and has since I bought it. Replaced orings with no change. Like I said it does this most of the time but not all of the time. It starts with a rough idle then the popping noise. On the highway it runs a little rough and puffs out white smoke but not in a consistent or what I would consider a rhythmic manner. I took the air cleaner off and noticed that my cdr is spraying what looks like fuel in the intake more so on the passenger side than the left which doesn't make sense to me as the fuel is injected into the cylinder. I haven't been able to test injectors or compression as I don't have the tools or had the time yet. I've read head gasket as possible bleeding over pressure from one cylinder to another or injectors or ip. Any advice would be appreciated or experience with this problem. I'll try to upload a video when it's daylight out. Thank in advance.

Your CDR can't put fuel into the intake. Fuel, in no way, interacts with the CDR. It's either crankcase gasses or possibly a little bit of oil. Overall, it sounds, to me, like air is being sucked into your fuel lines. You did mention seeing bubbles in your glass filters. Air will cause a knock, rough running, and smoke. I think that if you fix this problem, the rest will disappear.

Yeah I read that somewhere. I removed the filters before this post and no change. Still could be air but not sure the way its acting. I get solid flow through the Schrader valve when I test fuel flow. Parked it for now was gonna pull the valve covers to check my lifters and rocker arms but the first bolt was so loose it spun easily so I tightened all of them down and they all took a few turns. Gonna mess around with it this weekend thank you for the response and will post updates

Maybe I misunderstood. If it was running, I would NOT mess with tightening the rocker arms.
I would change the valve cover gaskets if you are going to remove the covers.