Hey, I like how your project is going. I'm really slow at getting things done myself, but I'm fidgeting at the ideas I've been seeing and thinking of lately.
I really thought hard about mounting my Kenne Bell blower like the Eaton, with an IC underneath it. I began a thread about it on the SBFtech site I like so much. But over there the get snobby about some dreary SUV questions. I spent most of my posts explaining how tight our engine bays are, and how bad the exhaust is.
Anyway, I expect that your IC will solve your problems. You do have a small exhaust though, still. For a blown 4.0 engine, it should have a size nearing what a say 7.0 engine would need(assuming about 12psi(about 3/4 of 15psi)). Any engine pumping that much air should have an exhaust area comparable to dual 2.5" or dual 3" pipes. If you only have a single 2.5" exhaust now, that is creating a lot of back pressure as it is. Keep the two banks separate, and feed two cats, and two mufflers. That will likely be no louder than now(I'd yank the resonator too), and it'll need more fuel(it'll be lean without new tuning).
Keep at it, I love it.