Keep in mind that not all dynos are going to read the same HP. Which is why its better to compare before and after, lateral acceleration G's, and 1/4 mile times than peak HP/TQ numbers.
That said looking through your setup I have a few suggestions.
First and foremost you HAVE to pick parts that are designed to work TOGETHER. Do you think Ferrari, Porsche, lambo, etc randomly guesses what size cam lobes to use, how much compression, the size of their TB's, etc?
Of course not, its all very calculated, everything is designed to work efficiently for that engine. You have to do the same if you want to see power.
12.3:1 on stage 2 cams sounds like seriously undercaming the engine. I will have to look around for the ABDC spec on the stage 2's, but I know people running that much CR on toda spec c's.
The DC 4-2-1 has a 2" collector, not even a 2.25" (like most people think). This is going to SERIOUSLY bottleneck your exhaust. I would bet you have some nasty backpressure. Look into a header with a 2.5" collector.
The skunk2 IM is design for the ITR cams and powerband (as its mostly an ITR replica). If you want to use it with much more aggressive cams (like the S2S2's are) you either need a manifold with shorter runners, larger plenum, and larger runners, or to send that manifold to Energy Dynamics to have it cut open and hogged out.
Larry mentions he often removes 3lbs of material from those manifold to get them to flow for the high HP guys.