Hi, welcome to JustAnswer! This is Ed.
You probably have a mechanical problem. Either it's a bad pin in the MDS lifter that is slipping out, or the lifter base (roller) has lost inner bearing pins. Either way, it's going to affect intake charge and engine compression.
What I'd suggest would be to take a compression test during the moments when the engine is running its worst.
If the problem is with an MDS pin, you will have absolutely ZIP for compression. NADA, nothing. If that number increases later when the engine is running OK, it strongly suggests that the problem is with the multiple displacement system and the intake valve isn't being lifted at all. This sort of thing doesn't seem likely with a worn-out lifter roller, which will constantly change engine compression depending on when the high and low spots of the lifter change.
Worn-out lower lifter rollers tend to follow an almost elliptical path, not following the camshaft profile as they should. At one cycle, they may be on the low part of the roller (which has needle bearings INSIDE the contact roller), allowing decent lift and valve closure. The next cycle the roller may push the lifter fully-up, holding the valve open because the hydraulic portion of the lifter has compensated for lash adjustment. Misfire occurs mostly when the valve can't close and that may vary with engine speed.
Camshafts are being destroyed with fair regularity on Hemi engines these days because of this sort of problem. Be wary of engine compression variances between cylinders for comparison and be prepared to do a full camshaft replacement if you see this sort of situation.