Trae I checked out the videos you did with the motor sound and there's definitely something there.
A few things to do if I was in your predicament is;
Change fuel supplier(Texaco,Valero,Flying J,etc)
Add fuel additive like PSDK,Lucas,Diesel treat,etc
Check fuel pressure(we gotta do that)
Change fuel filter(I change every 8K-10K)
Where you at as far as motor oil(mileage)
Change Motor Oil brand(could be suspect)
Do a Blackstone analysis with additive analysis ($25-$30) results within a week
Perhaps install a 203 thermo(helped reduce engine clatter during winter months with our 7.3L)
Dunno if you did the in tank fuel mod(could have air intrusion in the fuel supply from the tank)
Too much advance on the blue CPS? Maybe switch back to the stocker for S & G's ?
Those would be the things I'd go over with our 7.3L for the most part.