Pros - Better flow, bigger more straight runners.
Cons - Without cams or considerable mods, an IM isn't going to help much.
But, I think you're up to something quite tricky so an intake mainfold would be a good mod to do. Stock 1st gen B16 has a relativley tiny inake manifold, even compared to newer B16s. You will lose your fast idle control valve though. You don't drive that car in the winter anyway, do you?
Give consideration to find a used ITR intake manifold if thats something you could do. For the price they sell for you're not going to get better gains for the extra $$ spent on a new Skunk2 manifold. (hp for dollar)
Sidenote: I almost laugh when I get to see the tiny IM on D series motors.. Especially DXs. They're funny.