Now that I see what you're talking about, you ain't kidding. That's rough.
Since it goes away after a while you know it's not permanent damage. If you drive it like that does it try to race away from you? Like a tiny bump on the pedal and the engine tries to run wide open. If so that's air intrusion. (I'm guessing not though.)
After that is maybe an injector leaking down or sticking open.
Or a collapsed lifter that eventually fills back up. I've never dealt with that yet.
There is a bit of surging if I try to drive it when it is doing that, but more of a lack of power than any uncontrollable acceleration. Like the surge is more like the engine slows than the engine takes off.
So far I've replaced the o rings on all of the injectors where the return caps were leaking, that dried all of that up. The only remaining one that might be an issue is the one directly under the fuel filter. That one had fuel and dust stuck to it (the return cap, the metal fuel line, etc.), kinda like fuel might've been spraying out there. I really doubt it is the o rings on the return line so I'm kinda lost. That injector has a metal piece above it, between the top of the injector and the metal fuel line nut, kinda confusing. I'll attach a photo. It is almost like a coupling but I have no idea why it would be there.
I don't think it is anything to do with the fuel filter or the housing, everything up there is dry.
Do I need to worry about running the truck? I'm worried I might be damaging it while this issue clears up as the truck warms up.
Incase this didn’t make sense, the return system is not your supply side. You can run the engine with no caps and o rings if you wanted to it would just be messy. Things that sound like a gas knock on this engine that then go away is usually supply side air intrusion. Other things that can make it sound knocky but not internal mechanical are timing way off, bad injector (this sounds a bit different than the air). A lifter that’s lazy but I wouldn’t describe it as a knock. A rod knock in the bottom end sounds like a deep knocking and a lifter sounds like a higher tapping in the top end.
Can you catch us up and summarize what troubleshooting and diagnostic steps you took so far?
Okay I assumed that since the fuel return goes back to the filter and back to the tank there could be air in the lines from the return side.
To be clear the roughness upon startup is greater the longer the truck has sat. For example, if it sits 6 hours and gets cold (I assume it is getting cold when it is 20 or so outside and it is sitting outside for 6 hours), it'll rattle a little. If it sits 24 hrs it'll rattle like it is falling apart. If it sits an hour or so, or maybe even a couple hours, I will have absolutely no rattle and it runs fine.