Why is Pro Stock Dodge down on horsepower ?

AJ not being competitive is a result of engine archetechture. The Hemi's intake valve is on the intake side of the chamber, and the GM stuff has it's valve on the side of the chamber. This makes for a longer intake tract on the GM engines, and with the hood rules, they are able to tune for the 10.5K rev limit. The shorter intake was why the Dodge was revving 500 or so RPM higher under the old rules.
For any given length of intake runner, there is a "resonant" RPM where they work best. Look no further than the Ramcharger Plymouth. That huge, long intake was to ram the charge into the cylinder at around 5000 rpm, about as high as the tech of the day allowed. Now, the "tunnel ram" manifolds are much shorter, and work at a much higher RPM.