I would not use CME if you want something decent. It is very easy these days to stroke anything and make decent power. "Decent meaning upwards of 1hp/inch, on engines that are 450-500". Including using stock parts like an intake and exhaust manifolds. So if that's what you want, find a builder that can do that for you. The price of $8K is close. The last 496 I did was $8500 with me supplying the core. An RB version quoted just after that was $9500 with aluminum heads and some dyno using stock exhaust manifolds.
On the intake - it is not rocket science to modify the shaker base to fit. You can buy a repro base, and have it modified to place the sealing flange where you need it with most manifolds that are slightly taller. Or run the factory intake. You will give up power, but something making 540 pound feet of torque will probably make you forget about the 20hp the intake is costing.