Intake was removed to clean?
You did a compression test but did not inform folks here? THIS is key stuff! Further, what were the results? (when was it done?)
And, again, what is up with the "grenade" comment? ALSO a KEY bit here. BAD NOISES _AND_ UNABLE TO PROPERLY REV UP screams BIG PROBLEMS.
Remove the serpentine belt and see if that makes the noise go away. If the noise persists then pop the valve cover and look for signs of valve impact (hammered lifters).
The engine could have been needing head work when the dealer dealt with it. OR, if could now need head work because of the work the dealer did; OR, perhaps something YOU did. There's been so much activity here, and multiple hands touching this car that it's going to take a lot of work to ASSESS what's really at the bottom of this.
Might start looking to get your hands on TB tools. Only real way to determine whether the TB job was done correctly: if the engine were running good then one can likely reason that things were done correctly; but, since the engine doesn't run well then there's a call for an assessment of the job.