As you already assumed, it's matter of going down the check list till you find it.
I had a squeak that drove me absolutely crazy. Me and my passengers came to the conclusion it was under the passenger side front suspension.

Never found it. Till I happened to lean on my driver's side swing box that's mounted at the end of my bed, and heard that same damn squeak. A little grease and it was gone for good.

I still can't explain how that noise went thru the tonneau cover and sounded like something under the front end on the opposite side!
Basically what I'm saying is, check the things you would normally think there's no way that it could be causing the noise. You never know!

Good luck bud. Mysterious noises drive my nuts.

 

I had similar rattles on take off.

Does it do it when you sit in park and rev or only in motion?

Mine only did it in motion. Turned out to be my IWE lines.

I also had a rattle on my FX4 where the skid plate underneath had lost one bolt and the other was barely hanging on.
Tightened it up and it went away.